Chromate reduction by cell-free extract of Bacillus firmus KUCr1

Microbial enzymatic reduction of a toxic form of chromium [Cr(VI)] has been considered as an effective method for bioremediation of this metal. This study reports on the in vitro reduction of Cr(VI) using cell-free extracts from a Cr(VI) reducing Bacillus firmus KUCr1 strain. Chromium reductase was found to be constitutive and its activity was observed both in soluble cell fractions (S12 and S150 and membrane cell fraction (P150). The reductase activity of S12 fraction was found to be optimal at 40 microM Cr(VI) with enzyme concentration equivalent to 0.493 mg protein/ml. Enzyme activity was dependent on NADH or NADPH as electron donor; optimal temperature and pH for better enzyme activity were 70 degrees C and 5.6, respectively. The Km value of the reductase was 58.33 microM chromate having a V(max) of 11.42 microM/min/mg protein. The metabolic inhibitor like sodium azide inhibited reductase activity of membrane fraction of the cell-free extract. Metal ions like Cu2+, Co2+, Ni2+ and As3+ stimulated the enzyme but others, such as Ag+, Hg2+, Zn2+, Mn2+, Cd2+ and Pb2+, inhibited Cr(VI) reductase activity.     

The bacterial virulence factor NleA inhibits cellular protein secretion by disrupting mammalian COPII function

Enterohemorrhagic and enteropathogenic Escherichia coli (EHEC and EPEC) maintain an extracellular lifestyle and use a type III secretion system to translocate effector proteins into the host cytosol. These effectors manipulate host pathways to favor bacterial replication and survival. NleA is an EHEC/EPEC- and related species-specific translocated effector protein that is essential for bacterial virulence. However, the mechanism by which NleA impacts virulence remains undetermined. Here we demonstrate that NleA compromises the Sec23/24 complex, a component of the mammalian COPII protein coat that shapes intracellular protein transport vesicles, by directly binding Sec24. Expression of an NleA-GFP fusion protein reduces the efficiency of cellular secretion by 50%, and secretion is inhibited in EPEC-infected cells. Direct biochemical experiments show that NleA inhibits COPII-dependent protein export from the endoplasmic reticulum. Collectively, these findings indicate that disruption of COPII function in host cells contributes to the virulence of EPEC and EHEC.     

Studies on synonymous codon and amino acid usage biases in the broad-host range bacteriophage KVP40

In this study, the relative synonymous codon and amino acid usage biases of the broad-host range phage, KVP40, were investigated in an attempt to understand the structure and function of its proteins/protein-coding genes, as well as the role of its tRNAs. Synonymous codons in KVP40 were determined to be ATrich at the third codon positions, and their variations are dictated principally by both mutational bias and translational selection. Further analysis revealed that the RSCU of KVP40 is distinct from that of its Vibrio hosts, V. cholerae and V. parahaemolyticus. Interestingly, the expression of the putative highly expressed genes of KVP40 appear to be preferentially influenced by the abundant host tRNA species, whereas the tRNAs expressed by KVP40 may be required for the efficient synthesis of all its proteins in a diverse array of hosts. The data generated in this study also revealed that KVP40 proteins are rich in low molecular weight amino acid residues, and that these variations are influenced primarily by hydropathy, mean molecular weight, aromaticity, and cysteine content.     

Population Variability of the FimH Type 1 Fimbrial Adhesin in Klebsiella pneumoniae

FimH is an adhesive subunit of type 1 fimbriae expressed by different enterobacterial species. The enteric bacterium Klebsiella pneumoniae is an environmental organism that is also a frequent cause of sepsis, urinary tract infection (UTI), and liver abscess. Type 1 fimbriae have been shown to be critical for the ability of K. pneumoniae to cause UTI in a murine model. We show here that the K. pneumoniae fimH gene is found in 90% of strains from various environmental and clinical sources. The fimH alleles exhibit relatively low nucleotide and structural diversity but are prone to frequent horizontal-transfer events between different bacterial clones. Addition of the fimH locus to multiple-locus sequence typing significantly improved the resolution of the clonal structure of pathogenic strains, including the K1 encapsulated liver isolates. In addition, the K. pneumoniae FimH protein is targeted by adaptive point mutations, though not to the same extent as FimH from uropathogenic Escherichia coli or TonB from the same K. pneumoniae strains. Such adaptive mutations include a single amino acid deletion from the signal peptide that might affect the length of the fimbrial rod by affecting FimH translocation into the periplasm. Another FimH mutation (S62A) occurred in the course of endemic circulation of a nosocomial uropathogenic clone of K. pneumoniae. This mutation is identical to one found in a highly virulent uropathogenic strain of E. coli, suggesting that the FimH mutations are pathoadaptive in nature. Considering the abundance of type 1 fimbriae in Enterobacteriaceae, our present finding that fimH genes are subject to adaptive microevolution substantiates the importance of type 1 fimbria-mediated adhesion in K. pneumoniae.Klebsiella pneumoniae is recognized as an important opportunistic pathogen that frequently causes urinary tract infections (UTI), septicemia, or pneumonia, particularly in immunocompromised individuals (25). K. pneumoniae is responsible for up to 10% of all nosocomial bacterial infections (12, 35). In recent years, a high incidence of community-acquired K. pneumoniae pyogenic liver abscess with a high mortality rate has been reported, especially from Taiwan, but also from other Asian countries, Europe, and North America (6, 8, 19, 27, 44). Furthermore, 15% to 30% of K. pneumoniae isolates are resistant to broad-spectrum cephalosporins via plasmid-encoded extended-spectrum β-lactamases (5).In contrast to many other bacterial pathogens, K. pneumoniae is ubiquitous in nature. Its nonclinical habitats include environmental locations, such as vegetation, soil, and surface waters, as well as transient commensal colonization of mucosal surfaces in humans and other animals (1). Several studies have reported K. pneumoniae isolates of environmental origin to be nearly identical to clinical isolates with respect to several phenotypic properties (16, 22, 23, 25, 30). It has been suggested that environmental isolates of K. pneumoniae may be as virulent as clinical isolates (24, 39).Several virulence factors have been identified in K. pneumoniae (25, 38). The prominent polysaccharide capsule expressed by most isolates, together with the lipopolysaccharide layer, protects the bacteria against phagocytosis and the bactericidal activity of serum. Fimbrial adhesins expressed by the bacteria are protein structures able to recognize molecular receptors and to facilitate adherence to specific tissue surfaces in the host. K. pneumoniae produces two major fimbrial adhesion organelles, type 1 and type 3 fimbriae (9). Type 1 fimbriae have mannose-sensitive hemagglutinins, while type 3 fimbriae have mannose-resistant hemagglutinins (21).Type 1 fimbriae are the most common adhesive organelle in Enterobacteriaceae and have been most extensively studied in Escherichia coli. The type 1 fimbrial structures of K. pneumoniae are homologous to those of E. coli with regard to genetic composition and regulation (37). Type 1 fimbriae and the adhesive subunit FimH, in particular, play an important role in UTI caused by both K. pneumoniae and E. coli (3, 15, 17, 30, 37). Analysis of E. coli fimH variation at the population level has revealed that the FimH adhesin in urinary E. coli isolates accumulates amino acid replacements that increase its tropism toward the uroepithelium and various components of basement membranes (14, 26, 31, 33, 46). Most of the replacements increase the monomannose binding capability of FimH under low shear by altering allosteric catch bond properties of the protein (40). The natural FimH mutants were shown to provide an advantage in colonization of the urinary tract in a mouse model (32) and correlate with the overall extraintestinal virulence of E. coli (11). Thus, FimH mutations are pathoadaptive in nature. No such population-wide analysis has been performed for K. pneumoniae fimH.Population genetic analysis involves comparison of the nucleotide and structural variability of the locus of interest across multiple bacterial strains of different clonalities and geographic origins. The clonal structure of the strains can be determined by multiple-locus sequence typing (MLST), in which 400- to 500-bp sequences of multiple genetically unlinked loci are determined in order to define the phylogenetic relationship of the strains and the extent of interclonal gene recombination (horizontal gene transfer). MLST has been used to reveal the epidemiological relationship of ceftazidime- and ciprofloxacin-resistant K. pneumoniae isolates of nosocomial origin (4). In addition, the analysis of gene variability enables the determination of the type of selection processes acting on loci of interest, with possible identification of mutational changes of functional significance that could enhance the organism''s ability to cause disease, i.e., that could be of a pathoadaptive nature.In this study, the population dynamics of the K. pneumoniae FimH adhesin were determined by analysis of fimH allelic diversity in strains of environmental and various clinical origins in the context of K. pneumoniae clonal structure based on the allelic diversity of three loci—tonB, mdh and fumC—commonly used for MLST.     

A study of phenotypic correlation with the genotypic status of HTM regions of KRTHB6 and KRTHB1 genes in monilethrix families of Indian origin

We investigated 21 affected individuals in two unrelated monilethrix families of Indian origin and identified point mutation (g.4624G>A) in the HTM motif (exon-7) of the KRTHB6 gene in all the affected members leading to E413K change in this basic keratin. The HTM motif of KRTHB1, however, showed previously unreported two allelic variants, one with three novel variations (SNPs) in cis: g.4421insT (intronic); g.4461T>C (exonic); g.4485A>G (exonic) and second with only intronic variation (SNP) (g.4421insT). Interestingly, the two distinct phenotypes of: localized severe hair defect with beaded appearance confined to the scalp of all the affected members of Family 1 and of generalized unbeaded hair defect of moderate severity in Family 2, segregated in the two families, respectively, correlating with the two separate genotypes for the functionally critical HTM region of KRTHB1 gene in the background of E413K mutation in the KRTHB6 gene. Presence of E413K mutation in the HTM of KRTHB6 gene was not observed in the background of the allelic variant with three SNPs in KRTHB1 gene in homozygous condition in all the affected members of Family 1, affected with a localized but severe form of the disease. However, the same (E413K) mutation existed in the KRTHB6 gene in the background of the allelic variant with three SNPs in the KRTHB1 gene in homozygous condition, consistently in all the affected members of Family 2, where all its affected members showed the segregation of a milder form of the disease. Presence of both E413K mutation in the KRTHB6 and the variations in the KRTHB1 genes were not observed together in randomly selected 150 unaffected controls outside the two affected families. This is also the first report of HTM mutation of KRTHB6 gene in monilethrix cases of Indian origin and the first report of SNPs in the KRTHB1 gene in literature to our knowledge.     

Pressures in archaeal protein coding genes: a comparative study

Our studies on the bases of codons from 11 completely sequenced archaeal genomes show that, as we move from GC-rich to AT-rich protein-coding gene-containing species, the differences between G and C and between A and T, the purine load (AG content), and also the overall persistence (i.e. the tendency of a base to be followed by the same base) within codons, all increase almost simultaneously, although the extent of increase is different over the three positions within codons. These findings suggest that the deviations from the second parity rule (through the increasing differences between complementary base contents) and the increasing purine load hinder the chance of formation of the intra-strand Watson-Crick base-paired secondary structures in mRNAs (synonymous with the protein-coding genes we dealt with), thereby increasing the translational efficiency. We hypothesize that the ATrich protein-coding gene-containing archaeal species might have better translational efficiency than their GC-rich counterparts.     

Inactivation and reactivation of phosphoprotein phosphatase

Summary The catalytic subunit of phosphoprotein phosphatase (Mr = 35 000) is inactivated by phosphate compounds such as trimetaphosphate, PPi, and ATP. The inactivation of phosphoprotein phosphatase by these phosphate compounds is time- and concentration-dependent, is not reversed by dilution or gel filtration and is protected by Pi. A dissociation constant for the enzyme-trimetaphosphate complex and a rate constant for the reaction were calculated to be 4.6 × 10^–4 M and 0.29 min ¹, respectively. The inactivation of phosphatase by PPi and ATP shows more complex kinetics than that by trimetaphosphate. The addition of EDTA to PPi and ATP exhibits more potent inactivation, even though EDTA alone does not inactivate phosphatase. This phosphoprotein phosphatase is not labeled by [-³²P]ATP. The inactivation of phosphatase by PPi or ATP can only be reversed by Mn²⁺ or Co²⁺, among all other metals or cationic compounds tried. The reactivation also requires sulfhydryl compounds. The effectiveness of sulfhydryl compounds follows the order: dithioerythritol > mercaptoethanol > cysteine. Glutathione was without effect. Metal analysis of the catalytic subunit did not reveal any significant amounts of Ca, Cd, Co, Cu, Fe, Mg, Mn, Ni, Sn, or Zn. Phosphoprotein phosphatase activity from zinc-deficient rat livers also eliminated the possibility of this phosphatase being a zinc metalloenzyme. Inactivation does not seem to be due to a loss of a critical metal ion. Other mechanisms for inactivation are presented.Abbreviations used EDTA Ethylenediamine tetraacetic acid - PPi Inorganic pyrophosphate - DTE Dithioerythritol. To whom requests for reprints should be addressed.     

Cnidae in the sea anemone Sagartiogeton viduatus (Muller, 1776) (Cnidaria,Anthozoa); A comparison to cnidae in the sea anemone Metridium senile (Linnaeus, 1761) (Cnidaria,Anthozoa)

The cnidom of the sea anemone Sagartiogeton viduatus (Muller, 1776) is described from interference‐contrast light micrographs (LMs) and scanning electron micrographs (SEMs). Special attention is given to nematocyst maturation, including the differentiation of the shaft into proximal and main regions as helical folding of the shaft wall proceeds. Comparisons are made with Metridium senile (Linnaeus, 1761), whose cnidom, with a few exceptions, is closely similar to that of S. viduatus. The two anemones possess b‐ and p‐mastigophores, p‐amastigophores, isorhizas and spirocysts. Although the majority of cnidae in S. viduatus is smaller than corresponding ones in M. senile, they are grouped into the same size classes as those of M. senile, namely small, medium and large. The main differences from M. senile cnidae are the followings: (1) Large acontia p‐amastigophores are the largest nematocysts in S. viduatus. (2) They are noticeably larger than the large acontia b‐mastigophores, and (3) they are separated from the p‐amastigophores of M. senile by the sinusoid pattern of their U‐shaped capsular matrix. (4) The large acontia b‐mastigophores are microbasic and not mesobasic as in M. Senile, and (5) they do not produce darts. (6) Another difference from M. senile is the absence of catch‐tentacle isorhizas.     

22q11.2 distal deletion: a recurrent genomic disorder distinct from DiGeorge syndrome and velocardiofacial syndrome

Microdeletions within chromosome 22q11.2 cause a variable phenotype, including DiGeorge syndrome (DGS) and velocardiofacial syndrome (VCFS). About 97% of patients with DGS/VCFS have either a common recurrent ~3 Mb deletion or a smaller, less common, ~1.5 Mb nested deletion. Both deletions apparently occur as a result of homologous recombination between nonallelic flanking low-copy repeat (LCR) sequences located in 22q11.2. Interestingly, although eight different LCRs are located in proximal 22q, only a few cases of atypical deletions utilizing alternative LCRs have been described. Using array-based comparative genomic hybridization (CGH) analysis, we have detected six unrelated cases of deletions that are within 22q11.2 and are located distal to the ~3 Mb common deletion region. Further analyses revealed that the rearrangements had clustered breakpoints and either a ~1.4 Mb or ~2.1 Mb recurrent deletion flanked proximally by LCR22-4 and distally by either LCR22-5 or LCR22-6, respectively. Parental fluorescence in situ hybridization (FISH) analyses revealed that none of the available parents (11 out of 12 were available) had the deletion, indicating de novo events. All patients presented with characteristic facial dysmorphic features. A history of prematurity, prenatal and postnatal growth delay, developmental delay, and mild skeletal abnormalities was prevalent among the patients. Two patients were found to have a cardiovascular malformation, one had truncus arteriosus, and another had a bicuspid aortic valve. A single patient had a cleft palate. We conclude that distal deletions of chromosome 22q11.2 between LCR22-4 and LCR22-6, although they share some characteristic features with DGS/VCFS, represent a novel genomic disorder distinct genomically and clinically from the well-known DGS/VCF deletion syndromes.