DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally employed long (400–800 bp) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intra-species genetic variation. We report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterise four million SNPs and four hundred thousand structural variants, many of which are previously unknown. Our approach is effective for accurate, rapid and economical whole genome re-sequencing and many other biomedical applications.

The hyperthermophilic Archaeon Sulfolobus solfataricus metabolizes glucose by a non-phosphorylative variant of the Entner-Doudoroff pathway. In this pathway glucose dehydrogenase and gluconate dehydratase catalyze the oxidation of glucose to gluconate and the subsequent dehydration of gluconate to 2-keto-3-deoxygluconate. 2-Keto-3-deoxygluconate (KDG) aldolase then catalyzes the cleavage of 2-keto-3-deoxygluconate to glyceraldehyde and pyruvate. The gene encoding glucose dehydrogenase has been cloned and expressed in Escherichia coli to give a fully active enzyme, with properties indistinguishable from the enzyme purified from S. solfataricus cells. Kinetic analysis revealed the enzyme to have a high catalytic efficiency for both glucose and galactose. KDG aldolase from S. solfataricus has previously been cloned and expressed in E. coli. In the current work its stereoselectivity was investigated by aldol condensation reactions between D-glyceraldehyde and pyruvate; this revealed the enzyme to have an unexpected lack of facial selectivity, yielding approximately equal quantities of 2-keto-3-deoxygluconate and 2-keto-3-deoxygalactonate. The KDG aldolase-catalyzed cleavage reaction was also investigated, and a comparable catalytic efficiency was observed with both compounds. Our evidence suggests that the same enzymes are responsible for the catabolism of both glucose and galactose in this Archaeon. The physiological and evolutionary implications of this observation are discussed in terms of catalytic and metabolic promiscuity.The hyperthermophilic Archaeon Sulfolobus solfataricus grows optimally at 80 -85°C and pH 2-4, utilizing a wide range of carbon and energy sources (1). It has become one of the most comprehensively researched model organisms of archaeal metabolism and bioenergetics (2). Central metabolism in this organism involves a modified Entner-Doudoroff pathway (3), production of acetyl-CoA by pyruvate:ferredoxin oxidoreductase (4), and the citric acid cycle coupled to oxidative phosphorylation (5). The modified Entner-Doudoroff pathway is a nonphosphorylative variant of the classic pathway and proceeds with no net production of ATP (Fig. 1). An analogous pathway has also been detected in the thermoacidophilic Archaea Sulfolobus acidocaldarius (6), Thermoplasma acidophilum (7), and Thermoproteus tenax (8), as well as strains of Aspergillus fungi (9, 10).The first reaction of the non-phosphorylative Entner-Doudoroff pathway involves the NAD(P)-dependent oxidation of glucose to gluconate, catalyzed by glucose dehydrogenase. Gluconate is then dehydrated by gluconate dehydratase to 2-keto-3-deoxygluconate (KDG), 1 which undergoes an aldolate cleavage to pyruvate and glyceraldehyde, catalyzed by KDG aldolase. Glyceraldehyde dehydrogenase then oxidizes glyceraldehyde to glycerate, which is phosphorylated by glycerate kinase to give 2-phosphoglycerate. A second molecule of pyruvate is produced from this by the actions of enolase and pyruvate kinase.Glucose dehydrogenase has previously been purified to homogenei...

The hyperthermophilic archaeon Sulfolobus solfataricus grows optimally above 353 K and can metabolize glucose and its C4 epimer galactose via a nonphosphorylative variant of the Entner±Doudoroff pathway involving catalytically promiscuous enzymes that can operate with both sugars. The initial oxidation step is catalysed by glucose dehydrogenase (SsGDH), which can utilize both NAD and NADP as cofactors. The enzyme operates with glucose and galactose at similar catalytic ef®ciency, while its substrate pro®le also includes a range of other ®ve-and six-carbon sugars. Crystals of the 164 kDa SsGDH homotetramer have been grown under a variety of conditions. The best crystals to date diffract to 1.8 A Ê on a synchrotron source, have orthorhombic symmetry and belong to space group P2 1 2 1 2. Attempts are being made to solve the structure by MAD and MR.