Microbial sugar transport systems and their importance in biotechnology

Insights into the glycerol transport of Yarrowia lipolytica

Cellular membranes separate cells from the environment and hence, from molecules essential for their survival. To overcome this hurdle, cells developed specialized transport proteins for the transfer of metabolites across these membranes. Crucial metabolites that need to cross the membrane of each living organism, are the carbon sources. While many organisms prefer glucose as a carbon source, the yeast Yarrowia lipolytica seems to favor glycerol over glucose. The fast growth of Y. lipolytica on glycerol and its flexible metabolism renders this yeast a fascinating organism to study the glycerol metabolism. Based on sequence similarities to the known fungal glycerol transporter ScStl1p and glycerol channel ScFps1p, ten proteins of Y. lipolytica were found that are potentially involved in glycerol uptake. To evaluate, which of these proteins is able to transport glycerol in vivo, a complementation assay with a glycerol transport‐deficient strain of Saccharomyces cerevisiae was performed. Six of the ten putative transporters enabled the growth of S. cerevisiae stl1Δ on glycerol and thus, were confirmed as glycerol transporting proteins. Disruption of the transporters in Y. lipolytica abolished its growth on 25 g/L glycerol, but the individual expression of five of the identified glycerol transporters restored growth. Surprisingly, the transporter‐disrupted Y. lipolytica strain retained its ability to grow on high glycerol concentrations. This study provides insight into the glycerol uptake of Y. lipolytica at low glycerol concentrations through the characterization of six glycerol transporters and indicates the existence of further mechanisms active at high glycerol concentrations.

Six proteins of Yarrowia lipolytica were identified as glycerol transporters.

Two channel proteins and four active transporters facilitated glycerol uptake.

Identified transporters are involved in glycerol uptake <25 g/L glycerol.

Indication of further glycerol transporters in Y. lipolytica was obtained.

Unravelling the Complex Duplication History of Deuterostome Glycerol Transporters

Transmembrane glycerol transport is an ancient biophysical property that evolved in selected subfamilies of water channel (aquaporin) proteins. Here, we conducted broad level genome (>550) and transcriptome (>300) analyses to unravel the duplication history of the glycerol-transporting channels (glps) in Deuterostomia. We found that tandem duplication (TD) was the major mechanism of gene expansion in echinoderms and hemichordates, which, together with whole genome duplications (WGD) in the chordate lineage, continued to shape the genomic repertoires in craniates. Molecular phylogenies indicated that aqp3-like and aqp13-like channels were the probable stem subfamilies in craniates, with WGD generating aqp9 and aqp10 in gnathostomes but aqp7 arising through TD in Osteichthyes. We uncovered separate examples of gene translocations, gene conversion, and concerted evolution in humans, teleosts, and starfishes, with DNA transposons the likely drivers of gene rearrangements in paleotetraploid salmonids. Currently, gene copy numbers and BLAST are poor predictors of orthologous relationships due to asymmetric glp gene evolution in the different lineages. Such asymmetries can impact estimations of divergence times by millions of years. Experimental investigations of the salmonid channels demonstrated that approximately half of the 20 ancestral paralogs are functional, with neofunctionalization occurring at the transcriptional level rather than the protein transport properties. The combined findings resolve the origins and diversification of glps over >800 million years old and thus form the novel basis for proposing a pandeuterostome glp gene nomenclature.

High lipid accumulation in Yarrowia lipolytica cultivated under double limitation of nitrogen and magnesium

Yarrowia lipolytica cultivated under double nitrogen and magnesium limitation, but not under single nitrogen or single magnesium limitation, produced 12.2g/l biomass containing 47.5% lipids, which corresponds to a lipid production 5.8g/l. These yields are the higher described in the literature for wild strains of Y. lipolytica. Transcription of ACL1 and ACL2, encoding for ATP-citrate lyase (ATP:CL) was observed even under non-oleaginous conditions but high activity of ATP:CL was only detected under oleaginous conditions induced by low or zero activity of NAD(+) dependent isocitrate dehydrogenase. The low activity of malic enzyme (ME), a NADPH donor in typical oleaginous microorganisms, indicated that ME may not be implicated in lipid biosynthesis in this yeast, and NADPH may be provided by the pentose phosphate pathway (PPP). These findings underline the essential role of magnesium in lipogenesis, which is currently quite unexplored. The presence of organic nitrogen in low concentrations during lipogenesis was also required, and this peculiarity was probably related with the PPP functioning, being the NADPH donor of lipogenic machinery in Y. lipolytica.

Unravelling the complete genome sequence of Advenella mimigardefordensis strain DPN7T and novel insights in the catabolism of the xenobiotic polythioester precursor 3,3'-dithiodipropionate

Advenella mimigardefordensis strain DPN7(T) is a remarkable betaproteobacterium because of its extraordinary ability to use the synthetic disulfide 3,3'-dithiodipropionic acid (DTDP) as the sole carbon source and electron donor for aerobic growth. One application of DTDP is as a precursor substrate for biotechnically synthesized polythioesters (PTEs), which are interesting non-degradable biopolymers applicable for plastics materials. Metabolic engineering for optimization of PTE production requires an understanding of DTDP conversion. The genome of A. mimigardefordensis strain DPN7(T) was sequenced and annotated. The circular chromosome was found to be composed of 4,740,516 bp and 4112 predicted ORFs, whereas the circular plasmid consisted of 23,610 bp and 24 predicted ORFs. The genes participating in DTDP catabolism had been characterized in detail previously, but knowing the complete genome sequence and with support of Tn5: :mob-induced mutants, putatively involved transporter proteins and a transcriptional regulator were also identified. Most probably, DTDP is transported into the cell by a specific tripartite tricarboxylate transport system and is then cleaved by the disulfide reductase LpdA, sulfoxygenated by the 3-mercaptopropionate dioxygenase Mdo, activated by the CoA ligase SucCD and desulfinated by the acyl-CoA dehydrogenase-like desulfinase AcdA. Regulation of this pathway is presumably performed by a transcriptional regulator of the xenobiotic response element family. The excessive sulfate that is inevitably produced is secreted by the cells by a unique sulfate exporter of the CPA (cation : proton antiporter) superfamily.

Genomics Perspectives of Bioethanol Producing Zymomonas Mobilis

In recent years, there has been continuous increase in demand for fossil fuels that has led to the need for new potential fuel sources. Biofuels, in particular ethanol, are of high interest because of dwindling fossil fuels. Among the ethanol producers, Zymomonas mobilis has acquired greater interest because it is a renewable source of bioethanol. Zymomonas mobilis is an aerotolerant, gram-negative, ethanol producing bacterium that shows high ethanol yield, tolerance, and greater productivity. This chapter focuses on recent efforts made to engineer Z. mobilis, transcriptomic, genome-based metabolomic studies, and bioinformatics exploitation of the available genomic data for the production of bioethanol. Recently, several bioinformatics tools have been used to predict the functional properties of the carbohydrate active ethanologenic enzymes in Z. mobilis. A number of processes were used to study the functional properties of the ethanologenic enzymes of Z. mobilis. Thus, functional genomics seeks to apply technologies that would help to improve the production of bioethanol by Z. mobilis.

A lipid-anchored binding protein is a component of an ATP-dependent cellobiose/cellotriose-transport system from the cellulose degrader Streptomyces reticuli

During cultivation in the presence of cellobiose or crystalline cellulose, Streptomyces reticuli expresses an inducible uptake system that transports cellobiose (K(m), 4 microM), cellotriose and, to a lesser degree, cellotetraose and cellopentaose. Cellobiose uptake is dependent on ATP and inhibited by N-ethylmaleimide. A binding protein was identified in its palmitylated form in the cytoplasmic membrane of mycelia. It could be extracted with the detergent Triton X-100 and purified by two subsequent anion-exchange chromatographies. It showed highest affinity (Kd, 1.5 microM) for cellobiose and cellotriose. The data suggest that cellobiose/cellotriose uptake is mediated by a membrane-anchored lipoprotein as a component of an ATP-binding-cassette-transporter system.

Analysis and modeling of substrate uptake and product release by prokaryotic and eukaryotic cells

Translocation of molecules and ions across cell membranes is an important step for a complete description of the metabolic network in terms of kinetics, energetics and control. With a few exceptions, most molecules cross the permeability barrier of the membrane with the aid of membrane-embedded carrier proteins. Uptake of nutrients (carbon, energy and nitrogen sources as well as supplements) and excretion of the majority of products are thus carrier-mediated transport processes. Consequently, they are characterized by particular kinetic properties of the respective carrier systems, they depend on energy sources (driving forces) which must be provided by the cell, and they are subject to regulation both on the level of activity and expression. They are thus fully integrated into the functional and regulatory networks of the cell. Structural (primary structure, conformation and topology) and functional properties (kinetics, energetics and regulation) of the different classes of carrier systems from both prokaryotic and eukaryotic membranes are summarized. The methodical requirements for a quantitative measurement of their function and possible pitfalls in transport studies are described, both for determination using isolated cells and for analysis in a bioreactor. The significance of transport reactions for biotechnological processes in general and for metabolic design in particular is discussed, with respect to nutrient uptake, product excretion and the occurrence of energy wasting combinations of transport reactions (futile cycles). Some examples are given where transport reactions have been incorporated into modeling approaches with respect to metabolic control, to flux analysis, to kinetic properties and to energetic demands.

Reconstruction of glucose uptake and phosphorylation in a glucose-negative mutant of Escherichia coli by using Zymomonas mobilis genes encoding the glucose facilitator protein and glucokinase

Expression of the Zymomonas mobilis glf (glucose facilitator protein) and glk (glucokinase) genes in Escherichia coli ZSC113 (glucose negative) provided a new functional pathway for glucose uptake and phosphorylation. Both genes were essential for the restoration of growth in glucose minimal medium and for acid production on glucose-MacConkey agar plates.

Cellular and metabolic engineering. An overview

Metabolic engineering is defined as the purposeful modification of intermediary metabolism using recombinant DNA techniques. Cellular engineering, a more inclusive term, is defined as the purposeful modification of cell properties using the same techniques. Examples of cellular and metabolic engineering are divided into five categories: 1. Improved production of chemicals already produced by the host organism; 2. Extended substrate range for growth and product formation; 3. Addition of new catabolic activities for degradation of toxic chemicals; 4. Production of chemicals new to the host organism; and 5. Modification of cell properties. Over 100 examples of cellular and metabolic engineering are summarized. Several molecular biological, analytical chemistry, and mathematical and computational tools of relevance to cellular and metabolic engineering are reviewed. The importance of host selection and gene selection is emphasized. Finally, some future directions and emerging areas are presented.

Binding-protein-dependent lactose transport in Agrobacterium radiobacter

Agrobacterium radiobacter NCIB 11883 was grown in lactose-limited continuous culture at a dilution rate of 0.045/h. Washed cells transported [14C]lactose and [methyl-14C]beta-D-thiogalactoside, a nonmetabolisable analog of lactose, at similar rates and with similar affinities (Km for transport, less than 1 microM). Transport was inhibited to various extents by the uncoupling agent carbonyl cyanide p-trifluoromethoxyphenylhydrazone, by unlabeled beta-galactosides and D-galactose, and by osmotic shock. The accumulation ratio for methyl-beta-D-thiogalactoside was greater than or equal to 4,100. An abundant protein (molecular weight, 41,000) was purified from osmotic-shock fluid and shown by equilibrium dialysis to bind lactose and methyl-beta-D-thiogalactoside, the former with very high affinity (binding constant, 0.14 microM). The N-terminal amino acid sequence of this lactose-binding protein exhibited some homology with several other sugar-binding proteins from bacteria. Antiserum raised against the lactose-binding protein did not cross-react with two glucose-binding proteins from A. radiobacter or with extracts of other bacteria grown under lactose limitation. Lactose transport and beta-galactosidase were induced in batch cultures by lactose, melibiose [O-alpha-D-galactoside-(1----6)alpha-D-glucose], and isopropyl-beta-D-thiogalactoside and were subject to catabolite repression by glucose, galactose, and succinate which was not alleviated by cyclic AMP. We conclude that lactose is transported into A. radiobacter via a binding protein-dependent active transport system (in contrast to the H+ symport and phosphotransferase systems found in other bacteria) and that the expression of this transport system is closely linked to that of beta-galactosidase.

Genetic modification of Zymomonas mobilis

The bacterium Zymomonas mobilis is a potentially useful organism for the commercial production of ethanol as it is capable of more than double the rate of alcohol production by yeast. However, industrial application of this bacterium has been restricted in part due to the disadvantages of its limited substrate range (glucose, fructose and sucrose) and by-product formation. Progress in strain improvement and genetic manipulation of this ethanologen is reviewed. Methodologies for gaining reproducible gene transfer in Z. mobilis have recently been developed. Genetic modification has led to its growth on the additional substrates lactose and mannitol. Additionally, a range of by-product negative mutants have also been isolated. Further interest has focused on transfer of Z. mobilis genes to other fermentive organisms in order to gain enhanced product formation. Overall, these genetic approaches should lead to development of novel strains of Z. mobilis and other genera, capable of the use of starch, cellulose and xylan in a manner attractive for industrial ethanol production, besides facilitating over production of products from E. coli strains with enhanced capability to grow at high density.

Characterization of sugar uptake in wild-type Streptomyces clavuligerus, which is impaired in glucose uptake, and in a glucose-utilizing mutant

Wild-type Streptomyces clavuligerus NRRL 3585 is unable to utilize glucose. A glucose-utilizing (gut-1) mutant of S. clavuligerus NRRL 3585 has been obtained by N-methyl-N'-nitro-N-nitrosoguanidine mutagenesis. The gut-1 mutant is able to grow on glucose or galactose, while the wild type is unable to catabolize these hexoses. Similar binding affinities of glucose by cells of the wild type and the gut-1 mutant were found, but the wild type was unable to complete glucose transport. A soluble intracellular ATP-dependent (but not phosphoenolpyruvate-dependent) glucokinase activity was found both in the wild type and the gut-1 mutant. The gut-1 mutant has acquired a functional transport system that allows transport of glucose, 2-deoxyglucose, and galactose, as shown by hexose competition experiments. The gut-1 transport system concentrates glucose inside the cell at least 10- to 20-fold and is strongly inhibited by respiratory inhibitors, which prevent the establishment of a proton motive force, and by proton-conducting ionophores, suggesting that it is energized by a proton motive force. The new transport system is not completely sugar specific (transporting galactose and glucose through the same system), as opposed to the hexose-specific system reported in wild-type Streptomyces griseus.

Purification and properties of the gamma-butyrobetaine-binding protein from an Agrobacterium sp

A binding protein for gamma-butyrobetaine was purified from osmotic shock fluid of an Agrobacterium sp. It was a monomeric protein with an apparent molecular weight of 52,000 or 53,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration, respectively. The isoelectric point was 4.3, as determined by isoelectric focusing. Amino acid analysis of the protein showed that Asx and Glx were predominant components and that the protein contained no cysteine. The dissociation constant of this protein for gamma-butyrobetaine was found to be 0.7 microM by equilibrium dialysis. Attempts to sequence the amino-terminal end with the Edman method failed, suggesting that this region of the protein is blocked.