Expression, purification and use of the soluble domain of Lactobacillus paracasei beta-fructosidase to optimise production of bioethanol from grass fructans.

Microbial inulinases find application in food, pharmaceutical and biofuel industries. Here, a novel Lactobacillus paracasei beta-fructosidase was overexpressed as truncated cytosolic protein ((t)fosEp) in Escherichia coli. Purified (t)fosEp was thermostable (10-50 degrees C) with a pH optimum of 5; it showed highest affinity for bacterial levan (beta[2-6] linked fructose) followed by nystose, chicory inulin, 1-kestose (beta[2-1] linkages) and sucrose (K(m) values of 0.5, 15, 15.6, 49 and 398 mM, respectively). Hydrolysis of polyfructose moieties in agriculturally-sourced grass juice (GJ) with (t)fosEp resulted in the release of >13 mg/ml more bioavailable fructose than was measured in untreated GJ. Bioethanol yields from fermentation experiments with Brewer's yeast and GJ+(t)fosEp were >25% higher than those achieved using untreated GJ feedstock (36.5[+/-4.3] and 28.2[+/-2.7]mg ethanol/ml, respectively). This constitutes the first specific study of the potential to ferment ethanol from grass juice and the utility of a novel core domain of beta-fructosidase from L. paracasei.

TMCompare: transmembrane region sequence and structure.

UNLABELLED: TMCompare is an alignment and visualization tool for comparison of sequence information for membrane proteins contained in SWISS-PROT entries, with structural information contained in PDB files. The program can be used for: detection of breaks in alpha helical structure of transmembrane regions; examination of differences in coverage between PDB and SWISS-PROT files; examination of annotation differences between PDB files and associated SWISS-PROT files; examination and comparison of assigned PDB alpha helix regions and assigned SWISS-PROT transmembrane regions in linear sequence (one letter code) format; examination of these differences in 3D using the CHIME plugin, allowing; analysis of the alpha and non-alpha content of transmembrane regions. AVAILABILITY: TMCompare is available for use through selection of a query protein via the internet (http://www.membraneproteins.org/TMCompare) CONTACT: tmcompare@membraneproteins.org

Plant virus transmission by plasmodiophorid fungi is associated with distinctive transmembrane regions of virus-encoded proteins.

Computer analysis of published sequence data has consistently identified two complementary transmembrane domains in the coat protein readthrough domains of benyviruses, furoviruses and pomoviruses and in the P2 proteins of bymoviruses. These viruses differ in genome organisation but are all transmitted by plasmodiophorid fungi. The second domain is absent or disrupted in naturally-occurring deletion mutants that cannot be fungally-transmitted. In a non-transmissible substitution mutant of Beet necrotic yellow vein virus [Tamada et al. (1996) J Gen Virol 77: 1359-1367], the alignment of the helices is disrupted. From conserved patterns detected in transmembrane helix sequences and calculated relative helix tilts, structural arrangements consistent with tight packing of transmembrane helices were identified. These included ridge/groove arrangements between the two helices and strong electrostatic associations at the interfacial regions of the membrane. The data strongly suggest that these transmembrane helices facilitate the movement of virus particles across the fungal membrane.

Analysis of the pore of the unusual major intrinsic protein channel, yeast Fps1p.

Fps1p is a glycerol efflux channel from Saccharomyces cerevisiae. In this atypical major intrinsic protein neither of the signature NPA motifs of the family, which are part of the pore, is preserved. To understand the functional consequences of this feature, we analyzed the pseudo-NPA motifs of Fps1p by site-directed mutagenesis and assayed the resultant mutant proteins in vivo. In addition, we took advantage of the fact that the closest bacterial homolog of Fps1p, Escherichia coli GlpF, can be functionally expressed in yeast, thus enabling the analysis in yeast cells of mutations that make this typical major intrinsic protein more similar to Fps1p. We observed that mutations made in Fps1p to "restore" the signature NPA motifs did not substantially affect channel function. In contrast, when GlpF was mutated to resemble Fps1p, all mutants had reduced activity compared with wild type. We rationalized these data by constructing models of one GlpF mutant and of the transmembrane core of Fps1p. Our model predicts that the pore of Fps1p is more flexible than that of GlpF. We discuss the fact that this may accommodate the divergent NPA motifs of Fps1p and that the different pore structures of Fps1p and GlpF may reflect the physiological roles of the two glycerol facilitators.

Membrane topology of the Mep/Amt family of ammonium transporters.

The Mep/Amt proteins constitute a new family of transport proteins that are ubiquitous in nature. Members from bacteria, yeast and plants have been identified experimentally as high-affinity ammonium transporters. We have determined the topology of AmtB, a Mep/Amt protein from Escherichia coli, as a representative protein for the complete family. This was established using a minimal set of AmtB-PhoA fusion proteins with a complementary set of AmtB-LacZ fusions. These data, accompanied by an in silico analysis, indicate that the majority of the Mep/Amt proteins contain 11 membrane-spanning helices, with the N-terminus on the exterior face of the membrane and the C-terminus on the interior. A small subset, including E. coli AmtB, probably have an additional twelfth membrane-spanning region at the N-terminus. Addition of PhoA or LacZ alpha-peptide to the C-terminus of E. coli AmtB resulted in complete loss of transport activity, as judged by measurements of [14C]-methylammonium uptake. This C-terminal region, along with four membrane-spanning helices, contains multiple residues that are conserved within the Mep/Amt protein family. Structural modelling of the E. coli AmtB protein suggests a number of secondary structural features that might contribute to function, including a putative ammonium binding site on the periplasmic face of the membrane at residue Asp-182. The implications of these results are discussed in relation to the structure and function of the related human Rhesus proteins.

Analysis of the intestinal absorption of essential fatty acids in vivo in the rat.

The absorption and competition kinetics of the essential fatty acids (EFAs), linoleic acid (LA), alpha-linolenic acid (alphaLnA) and arachidonic acid (AA) in vivo were studied in the perfused rat jejunum. Uptake of each EFA on its own followed saturable kinetics at low luminal concentrations, suggesting a facilitative transport process, the affinity of which increased with chain length and degree of unsaturation. Absorption of one EFA was enhanced by low, whilst competitively inhibited by high, concentrations of a second EFA. Whereas LA and alphaLnA each interfered with the absorption of one another, both had little effect on AA. There was a strong inverse correlation between the relative unsaturation of an EFA and the change in Km of its absorption observed upon inhibition with another EFA. Overall, the results indicated a specific absorptive mechanism, probably involving a transport protein, the affinity of which increased with the degree of unsaturation of the EFA.

Characterization of the ileal Na+/bile salt co-transporter in brush border membrane vesicles and functional expression in Xenopus laevis oocytes.

The Na+/bile salt co-transporter of the pig ileal brush border membrane has been expressed in Xenopus laevis oocytes. Injection of pig ileal poly (A)+ RNA into oocytes resulted in the functional expression of an Na(+)-gradient-stimulated taurocholate uptake within 2-5 days. The expressed Na(+)-dependent taurocholate uptake exhibited saturation kinetics (apparent Km of 48 microM), and displayed similar competitive substrate inhibition by taurodeoxycholate as the native brush border Na+/bile salt co-transporter studied in pig ileal brush border membrane vesicles. Interestingly, injection of pig proximal and mid intestinal poly (A)+ RNA into oocytes also resulted in the expression of the Na+/bile salt co-transporter, though the Na(+)-dependent transport of bile salts does not occur in brush border membrane vesicles (BBMV) isolated from pig proximal and mid intestine. This suggests that the mRNA coding for the co-transporter is present in the enterocytes lining the whole length of the small intestine, but that the function is only expressed in the brush border of the distal small intestine. The transport of D-glucose into BBMV, and the transport of methyl-alpha-D-glucopyranoside (a non-metabolizable hexose derivative) into oocytes were used throughout the study as methods of confirming the integrity of vesicles and oocytes.