Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the sixth and the current seventh pandemics, respectively. Cholera researchers continually face newly emerging and reemerging pathogenic clones carrying diverse combinations of phenotypic and genotypic properties, which significantly hampered control of the disease. To elucidate evolutionary mechanisms governing genetic diversity of pandemic V. cholerae, we compared the genome sequences of 23 V. cholerae strains isolated from a variety of sources over the past 98 years. The genome-based phylogeny revealed 12 distinct V. cholerae lineages, of which one comprises both O1 classical and El Tor biotypes. All seventh pandemic clones share nearly identical gene content. Using analogy to influenza virology, we define the transition from sixth to seventh pandemic strains as a ''shift'' between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages. In contrast, transition among clones during the present pandemic period is characterized as a ''drift'' between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V. cholerae O139 and V. cholerae O1 El Tor hybrid clones. Based on the comparative genomics it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.genomic islands ͉ cholera toxin prophage ͉ lateral gene transfer

The first step in the replication of the plus-stranded poliovirus RNA is the synthesis of a complementary minus strand. This process is initiated by the covalent attachment of UMP to the terminal protein VPg, yielding VPgpU and VPgpUpU. We have previously shown that these products can be made in vitro in a reaction that requires only synthetic VPg, UTP, poly ( The Picornaviridae family of plus-strand RNA viruses includes a large number of pathogens with widely different host range and disease symptoms (38). At the same time, picornaviruses show a strong similarity in their gene organization and in the mechanism by which they replicate their genomes (58). An unusual feature of their genomes is the presence of a small protein VPg, covalently linked to the 5Ј end of the RNA. Virus replication in the infected host cell is a two-step process, carried out primarily by the viral RNA polymerase, in conjunction with other viral and possibly also cellular proteins. It takes place in small vesicles that are derived from the host's cellular membranes and with which the nonstructural proteins of the virus are associated. First, the incoming viral RNA is transcribed into complementary minus strands which are then used as templates for the synthesis of the progeny plus strands. Although the basic steps of replication are well known, very little is understood about the details of these processes and in particular about the exact functions of the cis-acting RNA structures contained within picornaviral RNAs (1). One of the important unanswered questions about minus-strand synthesis is how the viral RNA polymerase recognizes and selects only its own RNA as template among the many polyadenylated mRNAs that are present in the host cell (45).Poliovirus is perhaps the best known member of the Picornaviridae. Its RNA genome of about 7,500 nucleotides (nt) is composed of a long 5Ј-nontranslated region (NTR), a single open reading frame, a short 3ЈNTR, and a poly(A) tail (Fig. 1A) (32). The 5Ј-terminal UMP of the viral RNA is linked to the hydroxyl group of VPg by a phosphodiester bond (Fig. 1A) (2, 56). The 5ЈNTR consists of two independent domains. The first is a cloverleaf-like structure which is involved both in plus-strand RNA synthesis (3,4,24,70) and in the process of switching from translation to replication (18). The second is a large and complex structure, the internal ribosomal entry site (IRES) (28, 47), which promotes translation of a polyprotein. This polyprotein (Fig. 1A) contains a capsid region (P1) and two nonstructural domains (P2 and P3) (32). The initial cleavage of the polyprotein is carried out by proteinase 2A pro at the P1/P2 site (64). Most other cleavages are mediated by the activities of proteinase 3C pro and its precursor, 3CD pro (22,23,29,73). The proteins of the P2 domain are predominantly involved in inducing the biochemical and structural changes that occur in the infected cell (8), but 2CATPase is also essential for viral genome replication (49). Those of the P3 region are the ones most directly invol...

Phosphorylation of histone H3 at Ser10 increases chromatin accessibility to transcription factor NF-kappaB on a subset of genes involved in immune responses. Here we report that a bacterial pathogen abrogated phosphorylation of histone H3 to 'shape' the transcriptional responses of infected host cells. We identify the Shigella flexneri protein effector OspF as a dually specific phosphatase that dephosphorylated mitogen-activated protein kinases in the nucleus, thus preventing histone H3 phosphorylation at Ser10 in a gene-specific way. That activity of OspF enabled shigella to block the activation of a subset of NF-kappaB-responsive genes, leading to compromised recruitment of polymorphonuclear leukocytes to infected tissues. S. flexneri has thus evolved the capacity to precisely modulate host cell epigenetic 'information' as a strategy for repressing innate immunity.

Bacteria of Shigella spp. are responsible for shigellosis in humans. They use a type III secretion system to inject effector proteins into host cells and induce their entry into epithelial cells or trigger apoptosis in macrophages. We present evidence that the effector OspG is a protein kinase that binds various ubiquitinylated ubiquitin-conjugating enzymes, including UbcH5, which belongs to the stem cell factor SCF ␤-TrCP complex promoting ubiquitination of phosphorylated inhibitor of NF-B type ␣ (phospho-I B␣). Transfection experiments indicated that OspG can prevent phospho-I B␣ degradation and NF-B activation induced by TNF-␣ stimulation. Infection of epithelial cells by the S. flexneri wild-type strain, but not an ospG mutant, led to accumulation of phospho-I B␣, consistent with OspG inhibiting SCF ␤-TrCP activity. Upon infection of ileal loops in rabbits, the ospG mutant induced a stronger inflammatory response than the wild-type strain. This finding indicates that OspG negatively controls the host innate response induced by S. flexneri upon invasion of the epithelium.T he intestinal barrier is endowed with detection and defense mechanisms to achieve tolerance to commensal microorganisms and protection against invading microorganisms (1). Invasion by extracellular and intracellular pathogens is sensed by various signaling pathways converging to activate NF-B, a member of the Rel family of transcription factors involved in the activation of a large number of genes in response to pathogens, stress signals and proinflammatory cytokines (2). Under nonstimulating conditions, NF-B is retained in the cytoplasm through its association with inhibitory proteins (I Bs). A variety of signaling pathways activate I B kinases to phosphorylate I Bs, leading to ubiquitination of phospho-I Bs and their degradation by the proteasome (3), which allows translocation of NF-B to the nucleus, activation of NF-B-regulated genes, and establishment of an inflammatory response.Ubiquitination, resulting in the covalent attachment of the 76-residue ubiquitin to target proteins, involves three sequential steps performed by one ubiquitin-activating enzyme (E1), a limited number of ubiquitin-conjugating enzymes (E2s; also known as Ubc in enzyme designations), and a large number of ubiquitin-ligating enzymes (E3s), respectively (4). Each E3 recognizes a set of substrates and cooperates with one or a few E2s. The E3 complex SCF ␤-TrCP , which promotes ubiquitination of phospho-I B␣, consists of five proteins: the scaffold protein Cullin1, the adaptor protein Skp1, the RING domain protein Roc1, the E2 UbcH5b, and the F box protein ␤-TrCP, which interacts with phospho-I B␣ (5).Bacteria of Shigella spp. are the agent of shigellosis in humans, a disease characterized by the destruction of the colonic epithelium that is responsible for 1 million deaths per year (6). These bacteria use a type III secretion (TTS) system to enter epithelial cells and trigger apoptosis in macrophages (7). TTS systems comprise (i) a secretion apparatus that spans the...

No abstract

No abstract

Shigella flexneri is the most common cause of bacterial dysentery in low-income countries. Despite this, S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on serotyping reactions developed over half-a-century ago. Here we combine whole genome sequencing with geographical and temporal data to examine the natural history of the species. Our analysis subdivides S. flexneri into seven phylogenetic groups (PGs); each containing two-or-more serotypes and characterised by distinct virulence gene complement and geographic range. Within the S. flexneri PGs we identify geographically restricted sub-lineages that appear to have persistently colonised regions for many decades to over 100 years. Although we found abundant evidence of antimicrobial resistance (AMR) determinant acquisition, our dataset shows no evidence of subsequent intercontinental spread of antimicrobial resistant strains. The pattern of colonisation and AMR gene acquisition suggest that S. flexneri has a distinct life-cycle involving local persistence.DOI: http://dx.doi.org/10.7554/eLife.07335.001

Shigella sonnei is a human-adapted pathogen that is emerging globally as the dominant agent of bacterial dysentery. To investigate local establishment, we sequenced the genomes of 263 Vietnamese S. sonnei isolated over 15 y. Our data show that S. sonnei was introduced into Vietnam in the 1980s and has undergone localized clonal expansion, punctuated by genomic fixation events through periodic selective sweeps. We uncover geographical spread, spatially restricted frontier populations, and convergent evolution through local gene pool sampling. This work provides a unique, high-resolution insight into the microevolution of a pioneering human pathogen during its establishment in a new host population.enteric disease | drug resistance | phylogeography | genomics