Conversion of a phosphoseryl/threonyl phosphatase into a phosphotyrosyl phosphatase.

By use of the autophosphorylated epidermal-growth-factor receptor and the synthetic peptide RRLIE-DAEY(P)AARG, representing an autophosphorylation site of the transforming protein of Rous-sarcoma virus, it is demonstrated that the phosphotyrosyl phosphatase activity of the polycation-stimulated phosphatases is substantially increased by an enzyme-directed effect of ATP or PPi. Concomitant with this increase in phosphotyrosyl phosphatase activity, the phosphorylase phosphatase activity is decreased, thus dramatically changing the substrate specificity of these enzymes. The dephosphorylation of four different phosphotyrosyl sites of the epidermal-growth-factor receptor is neither consecutive nor at random, but a preferred dephosphorylation of the P1 site over the P3 greater than P2 greater than P4 sites is observed. This phosphatase activity represents a substantial fraction of the total phosphotyrosyl phosphatase activity in the post-mitochondrial supernatant of Xenopus laevis oocytes.     

Genome Sequence of the Emerging Pathogen Helicobacter canadensis

We determined the genome sequence of the type strain of Helicobacter canadensis, an emerging human pathogen with diverse animal reservoirs. Potential virulence determinants carried by the genome include systems for N-linked glycosylation and capsular export. A protein-based phylogenetic analysis places H. canadensis close to Wolinella succinogenes.Helicobacter canadensis is an emerging pathogen that has been isolated from four Canadian patients with diarrhea and an Australian patient with bacteremia (3, 10). Wild geese have been identified as a reservoir in Europe (12, 13), while in China, the organism has been isolated from the feces of wild rodents (5). H. canadensis has also been isolated from laboratory rabbits (11) and from Guinea fowl in France (8). Atypical isolates have been obtained from swine feces from The Netherlands and Denmark (6). To shed light on the virulence and colonization factors of H. canadensis and to reassess its phylogenetic status, we performed whole-genome sequencing of the type strain, H. canadensis strain MIT 98-5491/NCTC 13241.Single- and paired-end whole-genome shotgun sequencing was performed using 454 pyrosequencing technology, supplemented by Solexa sequencing. An initial assembly of the 454 single-end and paired-end data was created using a Newbler assembler (Roche), generating four scaffolds with an average size of 402 kb. The genome sequence was completed using a combination of BLASTX searches and analysis of the Solexa data, followed by confirmatory PCRs, PCR-assisted contig extension (1), and combinatorial PCR, with conventional and long-PCR protocols. Annotation was performed using GenDB (7).The genome of H. canadensis NCTC 13241 consists of a single circular chromosome 1,623,845 bp in length, with a G+C content of 34%. There are 1,535 protein-coding sequences (CDSs), 40 transfer RNAs, and three rRNA loci.Although phylogenetic analyses based on 16S rRNA gene sequences place H. canadensis in the genus Helicobacter (3), analysis of 23S rRNA sequences supports a clade containing H. canadensis and Wolinella succinogenes (2). Our own phylogenetic analysis using a concatenation of 482 conserved CDSs from the H. canadensis genome and related genomes provides strong support for a W. succinogenes/H. canadensis clade (data not shown), suggesting that the current taxonomy should be reevaluated.One hundred seventeen CDSs from H. canadensis have no detectable ortholog in eight other genome-sequenced epsilonproteobacteria. We found only one contiguous region of difference longer than 10 genes (ROD1; HCAN_0630-HCAN_0663). Most CDSs in ROD1 are of unknown function, although, curiously, the region carries three versions of asparagine synthetase and contains six homopolymeric tracts. A second region of difference (ROD2; HCAN_0479-HCAN_0496) shows homology to HHGI1, a pathogenicity island from Helicobacter hepaticus strain ATCC 51449 that contributes to virulence in H. hepaticus (4).The H. canadensis NCTC 13241 genome contains 29 potentially phase-variable genes with homopolymeric tracts, including several genes that, by homology, might be implicated in virulence, e.g., an immunoglobulin A protease (HCAN_0234) and two homologues of the vacuolating cytotoxin from Helicobacter pylori (HCAN_0457 and HCAN_714). The genome contains a capsular polysaccharide export locus similar to that in Campylobacter jejuni (9). Also, like C. jejuni, H. canadensis possesses genes encoding an N-linked glycosylation pathway, including two copies of PglB (HCAN_0729 and HCAN_0930).     

Tetratricopeptide repeats in the type III secretion chaperone, LcrH: their role in substrate binding and secretion

Non-flagellar type III secretion systems (T3SSs) transport proteins across the bacterial cell and into eukaryotic cells. Targeting of proteins into host cells requires a dedicated translocation apparatus. Efficient secretion of the translocator proteins that make up this apparatus depends on molecular chaperones. Chaperones of the translocators (also called class-II chaperones) are characterized by the possession of three tandem tetratricopeptide repeats (TPRs). We wished to dissect the relations between chaperone structure and function and to validate a structural model using site-directed mutagenesis. Drawing on a number of experimental approaches and focusing on LcrH, a class-II chaperone from the Yersinia Ysc-Yop T3SS, we examined the contributions of different residues, residue classes and regions of the protein to chaperone stability, chaperone-substrate binding, substrate stability and secretion and regulation of Yop protein synthesis. We confirmed the expected role of the conserved canonical residues from the TPRs to chaperone stability and function. Eleven mutations specifically abrogated YopB binding or secretion while three mutations led to a specific loss of YopD secretion. These are the first mutations described for any class-II chaperone that allow interactions with one translocator to be dissociated from interactions with the other. Strikingly, all mutations affecting the interaction with YopB mapped to residues with side chains projecting from the inner, concave surface of the modelled TPR structure, defining a YopB interaction site. Conversely, all mutations preventing YopD secretion affect residues that lie on the outer, convex surface of the triple-TPR cluster in our model, suggesting that this region of the molecule represents a distinct interaction site for YopD. Intriguingly, one of the LcrH double mutants, Y40A/F44A, was able to maintain stable substrates inside bacteria, but unable to secrete them, suggesting that these two residues might influence delivery of substrates to the secretion apparatus.     

Whole-genome sequence of the emerging pathogen Mycobacterium abscessus strain 47J26

Mycobacterium abscessus is a rapidly growing environmental mycobacterium commonly found in soil and water which is often also associated with infections in humans, particularly of the lung. We report herein the draft genome sequence of M. abscessus strain 47J26.     

EntrezAJAX: direct web browser access to the Entrez Programming Utilities

Web applications for biology and medicine often need to integrate data from Entrez services provided by the National Center for Biotechnology Information. However, direct access to Entrez from a web browser is not possible due to 'same-origin' security restrictions. The use of "Asynchronous JavaScript and XML" (AJAX) to create rich, interactive web applications is now commonplace. The ability to access Entrez via AJAX would be advantageous in the creation of integrated biomedical web resources. We describe EntrezAJAX, which provides access to Entrez eUtils and is able to circumvent same-origin browser restrictions. EntrezAJAX is easily implemented by JavaScript developers and provides identical functionality as Entrez eUtils as well as enhanced functionality to ease development. We provide easy-to-understand developer examples written in JavaScript to illustrate potential uses of this service. For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at