bluuebunny/crossref_metadata_2025 huggingface dataset:
Results From Malaysia’s 2016 Report Card on Physical Activity for Children and Adolescents
Authors: Sharif Razinah , Chong Kar Hau , Zakaria Nur Hadiyani , Ong Min Li , Reilly John J. , Wong Jyh Eiin , Saad Hazizi Abu , Poh Bee Koon
Published: November 2016

Background:

The 2016 Malaysia Active Healthy Kids Report Card aims to collect, assess, and grade current and comprehensive data on physical activity (PA) and associated factors in Malaysian children and adolescents aged 5 to 17 years.

Methods:

This report card was developed following the Active Healthy Kids Canada Report Card protocol. The Research Working Group identified the core matrices, assessed the key data sources, and evaluated the evidence gathered for grade assignments. A grade was assigned to each indicator by comparing the best available evidence against relevant benchmark using a standardized grading scheme.

Results:

Overall Physical Activity, Active Transportation, and Sedentary Behavior were assigned the D grade. The lowest grade of F was assigned to Diet, while School and Government Strategies and Investments were graded higher with a B. Five indicators were assigned INC (incomplete) due to a lack of representative data.

Conclusions:

The report card demonstrates that Malaysian children and adolescents are engaging in low levels of PA and active commuting, high levels of screen time, and have extremely low compliance with dietary recommendations. More efforts are needed to address the root causes of physical inactivity while increasing the opportunities for children and adolescents to be more physically active.
Results From South Africa’s 2016 Report Card on Physical Activity for Children and Youth
Authors: Uys Monika , Bassett Susan , Draper Catherine E. , Micklesfield Lisa , Monyeki Andries , de Villiers Anniza , Lambert Estelle V. , _ _
Published: November 2016

Background:

We present results of the 2016 Healthy Active Kids South Africa (HAKSA) Report Card on the current status of physical activity (PA) and nutrition in South African youth. The context in which we interpret the findings is that participation in PA is a fundamental human right, along with the right to “attainment of the highest standard of health.”

Methods:

The HAKSA 2016 Writing Group was comprised of 33 authorities in physical education, exercise science, nutrition, public health, and journalism. The search strategy was based on peer-reviewed manuscripts, dissertations, and ‘gray’ literature. The core PA indicators are Overall Physical Activity Level; Organized Sport Participation; Active and Outdoor Play; Active Transportation; Sedentary Behaviors; Family and Peer Influences; School; Community and the Built Environment; and National Government Policy, Strategies, and Investment. In addition, we reported on Physical Fitness and Motor Proficiency separately. We also reported on nutrition indicators including Overweight and Under-nutrition along with certain key behaviors such as Fruit and Vegetable Intake, and policies and programs including School Nutrition Programs and Tuck Shops. Data were extracted and grades assigned after consensus was reached. Grades were assigned to each indicator ranging from an A, succeeding with a large majority of children and youth (81% to 100%); B, succeeding with well over half of children and youth (61% to 80%); C, succeeding with about half of children and youth (41% to 60%); D, succeeding with less than half but some children and youth (21% to 40%); and F, succeeding with very few children and youth (0% to 20%); INC is inconclusive.

Results:

Overall PA levels received a C grade, as we are succeeding with more than 50% of children meeting recommendations. Organized Sports Participation also received a C, and Government Policies remain promising, receiving a B. Screen time and sedentary behavior were a major concern. Under- and over-weight were highlighted and, as overweight is on the rise, received a D grade.

Conclusions:

In particular, issues of food security, obesogenic environments, and access to activity-supportive environments should guide social mobilization downstream and policy upstream. There is an urgent need for practice-based evidence based on evaluation of existing, scaled up interventions.
Results From the Mozambique 2016 Report Card on Physical Activity for Children and Adolescents
Authors: Prista António , Daca Timoteo , Tchonga Francisco , Machava Eduardo , Macucule Cremildo , Ribeiro Edmundo
Published: November 2016

Background:

This article describes the procedures and development of the 2016 Mozambican Report Card on Physical Activity for Children and Adolescents.

Methods:

Following the procedures adopted in 2014 for that year’s report card, comprehensive searches on new data related to indicators of physical activity (PA) were done. A committee composed of physical activity and sports specialists graded each indicator consistent with the process and methodology outlined by the Active Healthy Kids Canada Report Card model.

Results:

Nine indicators of PA were graded. Compared with 2014 there were several differences which were caused by changes in the country as well as a more effective evaluation from the committee. The following grades were assigned: Overall Physical Activity Levels, C; Organized Sport Participation, F; Active Play, D; Active Transportation, C; Schools, D; Community and the Built Environment, F; and Government, F. Sedentary Behaviors and Family and Peers were graded Incomplete due to the lack of available information.

Conclusions:

The decline of the PA habits in urban centers reported in 2014 are accentuated and is influencing the rural areas in several ways. At present, there is no strategy or effective action from authorities to reverse this negative trend.
Results From Venezuela’s 2016 Report Card on Physical Activity for Children and Youth
Authors: Herrera-Cuenca Marianella , Méndez-Perez Betty , Morales Vanessa Castro , Martín-Rojo Joana , Tristan Bianca , Bandy Amilid Torín , Landaeta-Jiménez Maritza , Macías-Tomei Coromoto , López-Blanco Mercedes
Published: November 2016

Background:

The Venezuelan Report Card on Physical Activity for Children and Youth is the first assessment of information related to physical activity in Venezuela. It provides a compilation of existing information throughout the country and assesses how well it is doing at promoting opportunities for children and youth. The aim of this article is to summarize the information available.

Methods:

Thirteen physical activity indicators were graded by a committee of experts using letters A to F (A, the highest, to F, the lowest) based on national surveys, peer review studies, and policy documents.

Results:

Some indicators report incomplete information or a lack of data. Overweight and Obesity were classified as A; Body Composition and Nongovernmental Organization Policies as B; Municipal Level Policies as C; and Overall Physical Activity Levels and National Level Policies as D.

Conclusions:

63% of children and youth have low physical activity levels. Venezuela needs to undergo a process of articulation between the several existing initiatives, and for said purposes, political will and a methodological effort is required. Investments, infrastructure, and opportunities will be more equal for all children and youth if more cooperation between institutions is developed and communication strategies are applied.
Papers of note in
Science
Authors: VanHook Annalisa M.
Published: November 2016

This week’s articles highlight the involvement of a cytosolic DNA sensor in the response to radiation-induced DNA damage, a peptide that can inhibit tumor growth by causing a growth factor receptor to form amyloid aggregates, and the importance of endogenous RNA interference in maintaining cell quiescence.
Ultrastructural study of surface components of Streptococcus suis
Authors: Jacques M , Gottschalk M , Foiry B , Higgins R
Published: November 2016

The presence of capsular material on cells of nine reference strains of Streptococcus suis representing serotypes 1 to 8 and 1/2 was determined by transmission electron microscopy after polycationic ferritin labeling, immunostabilization, or fixation with a combination of glutaraldehyde and lysine. All the cells of the reference strains examined were covered with a layer of capsular material whose thickness varied between 20 to 30 nm and 350 to 375 nm when examined by immunostabilization. Capsular material from cells exposed to homologous antiserum was usually thicker than that from polycationic ferritin-labeled cells or cells fixed with glutaraldehyde-lysine. Negative staining revealed detectable surface structures on S. suis strains. All strains carried peritichous, thin, and flexible fimbriae with a diameter of approximately 2 nm and a length of up to 250 nm. This study indicated that morphological differences of surface structure exist among S. suis reference strains.
Escherichia coli metR mutants that produce a MetR activator protein with an altered homocysteine response
Authors: Byerly K A , Urbanowski M L , Stauffer G V
Published: November 2016

Using an Escherichia coli lac deletion strain lysogenized with a lambda phage carrying a metH-lacZ gene fusion, we isolated trans-acting mutations that result in simultaneous 4- to 6-fold-elevated metH-lacZ expression, 5- to 22-fold-lowered metE-lacZ expression, and 9- to 20-fold-elevated metR-lacZ expression. The altered regulation of these genes occurs in the presence of high intracellular levels of homocysteine, a methionine pathway intermediate which normally inhibits metH and metR expression and stimulates metE expression. P1 transductions and complementation tests indicate that the mutations are in the metR gene. Our data suggest that the mutations result in an altered MetR activator protein that has lost the ability to use homocysteine as a modulator of gene expression.
Continuous-culture study of the regulation of glucose and fructose transport in Kluyveromyces marxianus CBS 6556
Authors: Postma E , Van den Broek P J
Published: November 2016

Regulation of transport of D-glucose and D-fructose was studied in Kluyveromyces marxianus grown in continuous culture. Both substrates could be transported by at least two different transport systems, low-affinity transport and high-affinity proton-sugar symport. The low-affinity transporter, specific for both glucose and fructose, was constitutively present and was apparently not regulated by carbon catabolite repression. Regulation of the activity of the glucose- and fructose-specific proton symport systems appeared to proceed mainly through catabolite repression. Activation of symport did not need the presence of specific inductor molecules in the medium. Nevertheless, the capacities of the proton-sugar symporters varied in cells grown on a wide variety of carbon sources. The possibility that the control of proton symport activity is related to the presence of specific intracellular metabolites is discussed.
Cloning and nucleotide sequences of the genes for the subunits of NAD-reducing hydrogenase of Alcaligenes eutrophus H16
Authors: Tran-Betcke A , Warnecke U , Böcker C , Zaborosch C , Friedrich B
Published: November 2016

The genes hoxF, -U, -Y, and -H which encode the four subunit polypeptides alpha, gamma, delta, and beta of the NAD-reducing hydrogenase (HoxS) of Alcaligenes eutrophus H16, were cloned, expressed in Pseudomonas facilis, and sequenced. On the basis of the nucleotide sequence, the predicted amino acid sequences, and the N-terminal amino acid sequences, it was concluded that the structural genes are tightly linked and presumably organized as an operon, denoted hoxS. Two pairs of -24 and -12 consensus sequences resembling RpoN-activatable promoters lie upstream of hoxF, the first of the four genes. Primer extension experiments indicate that the second promoter is responsible for hoxS transcription. hoxF and hoxU code for the flavin-containing dimer (alpha and gamma subunits) of HoxS which exhibits NADH:oxidoreductase activity. A putative flavin-binding region is discussed. The 26.0-kilodalton (kDa) gamma subunit contains two cysteine clusters which may participate in the coordination of two [4F3-4S]centers. The genes hoxY and hoxH code for the small 22.9-kDa delta subunit and the nickel-containing 54.8-kDa beta subunit, respectively, of the hydrogenase dimer of HoxS. The latter dimer exhibits several conserved regions found in all nickel-containing hydrogenases. The roles of these regions in coordinating iron and nickel are discussed. Although the deduced amino acid sequences of the delta and beta subunits share some conserved regions with the corresponding polypeptides of other [NiFe] hydrogenases, the overall amino acid homology is marginal. Nevertheless, significant sequence homology (35%) to the corresponding polypeptides of the soluble methylviologen-reducing hydrogenase of Methanobacterium thermoautotrophicum was found. Unlike the small subunits of the membrane-bound and soluble periplasmic hydrogenases, the HoxS protein does not appear to be synthesized with an N-terminal leader peptide.
Characterization of transposon insertion out- mutants of Erwinia carotovora subsp. carotovora defective in enzyme export and of a DNA segment that complements out mutations in E. carotovora subsp. carotovora, E. carotovora subsp. atroseptica, and Erwinia chrysanthemi
Authors: Murata H , Fons M , Chatterjee A , Collmer A , Chatterjee A K
Published: November 2016

Soft-rotting Erwinia spp. export degradative enzymes to the cell exterior (Out+), a process contributing to their ability to macerate plant tissues. Transposon (Tn5, Tn10, Tn10-lacZ) insertion Out- mutants were obtained in Erwinia carotovora subsp. carotovora 71 by using plasmid and bacteriophage lambda delivery systems. In these mutants, pectate lyases, polygalacturonase, and cellulase, which are normally excreted into the growth medium, accumulated in the periplasm. However, localization of the extracellular protease was not affected. The Out- mutants were impaired in their ability to macerate potato tuber tissue. Out+ clones were identified in a cosmid library of E. carotovora subsp. carotovora 71 by their ability to complement mutants. Localization of cyclic phosphodiesterase in the periplasm indicated that the Out+ plasmids did not cause lysis or a nonspecific protein release. The Out+ derivatives of the E. carotovora subsp. carotovora 71 mutants regained the ability to macerate potato tuber tissue. Our data indicate that a cluster of several genes is required for the Out+ phenotype. While one plasmid, pAKC260, restored the Out+ phenotype in each of the 31 mutants of E. carotovora subsp. carotovora, E. carotovora subsp. atroseptica, and Erwinia chrysanthemi, it failed to render Escherichia coli export proficient. Homologs of E. carotovora subsp. carotovora 71 out DNA were detected by Southern hybridizations in subspecies of E. carotovora under high-stringency conditions. In contrast, E. chrysanthemi sequences bearing homology to the E. carotovora subsp. carotovora 71 out DNA were detectable only under low-stringency hybridization. Thus, although the out genes are functional in these two soft-rotting bacterial groups, the genes appear to have diverged.
Multiple translational products from a Mycoplasma hyorhinis gene expressed in Escherichia coli
Authors: Notarnicola S M , McIntosh M A , Wise K S
Published: November 2016

We analyzed protein expression from a cloned Mycoplasma hyorhinis genomic fragment that produces in Escherichia coli a set of related polypeptides of 110, 100, 65, and 55 kilodaltons from a coding region of just over 3.0 kilobases. Expression of these multiple products resulted from a mechanism operating at the translational level but not from truncation at UGA termination codons, which are known to encode tryptophan in several mycoplasma species. The structural relatedness of the proteins was demonstrated by two-dimensional tryptic peptic mapping, but their generation by posttranslational processing was ruled out by pulse-chase labeling analysis. Examination of proteins expressed from plasmid constructs and tryptic peptide analysis of these polypeptides and the original set of proteins revealed that they share carboxy-terminal regions, an observation inconsistent with truncation at UGA codons. Expression of proteins from this cloned fragment was not dependent on vector sequences and was observed when the coding region was placed under control of a T7 promoter, suggesting that all products were translated from a single message. Expression of related products in mycoplasmas was examined by immunoblot analysis of M. hyorhinis proteins with antiserum against overexpressed recombinant proteins. A single 115-kilodalton mycoplasma protein was detected, which is larger than any of the related proteins expressed in E. coli. Our analysis indicated that translation initiation sites are used in E. coli that are not active in mycoplasmas, thereby defining differences between the translational regulatory signals of mycoplasmas and eubacteria.
Complementation of an Escherichia coli proC mutation by a gene cloned from Treponema pallidum
Authors: Gherardini F C , Hobbs M M , Stamm L V , Bassford P J
Published: November 2016

Little is known concerning the biosynthetic and metabolic capabilities of the syphilis agent, Treponema pallidum, because of the inability to cultivate continuously the organism in vitro. To circumvent the problem of cultivation, researchers have used recombinant DNA technology to express treponemal protein antigens in Escherichia coli. However, with a few notable exceptions, the specific cellular roles of these cloned treponemal proteins have not been determined. In this study, a cosmid library of T. pallidum genomic DNA was constructed and amplified by repackaging infective lambda bacteriophage particles in vivo. Recombinant clones capable of complementing a null mutation in the E. coli proC gene encoding 1-pyrroline-5-carboxylate (P5C) reductase (EC 1.5.1.2) were subsequently identified. The complementing activity was eventually localized to a 2.3-kilobase BglII-HindIII fragment that hybridized to the same-size fragment of a BglII-HindIII digest of T. pallidum DNA. Two proteins of 41 and 27 kilodaltons (kDa) were encoded by this fragment, as determined by maxicell analysis. Although only the 41-kDa protein could be specifically precipitated by experimental syphilitic rabbit antisera, it was the 27-kDa protein that was responsible for the proC-complementing activity. The recombinant P5C reductase differed from the native E. coli enzyme by a number of biochemical properties. The cloning of a T. pallidum gene encoding P5C reductase strongly suggests that this pathogen has the ability to synthesize proline and possibly other amino acids.
The folding properties of the Escherichia coli maltose-binding protein influence its interaction with SecB in vitro
Authors: Weiss J B , Bassford P J
Published: November 2016

It has been proposed that the cytoplasmic SecB protein functions as a component of the Escherichia coli protein export machinery by serving as an antifolding factor that retards folding of the precursor maltose-binding protein (preMBP) into a translocation-incompetent form. In this study, it was found that SecB directly interacts with wild-type preMBP and various mutationally altered MBP species synthesized in vitro to form a SecB-MBP complex that can be precipitated with anti-SecB serum. The association of SecB with wild-type preMBP was relatively unstable; such a complex was formed only when SecB was present cotranslationally or after denaturation of previously synthesized preMBP and was detected with only low efficiency. In marked contrast, MBP species that were defective in the ability to assume the stable conformation of wild-type preMBP or that exhibited significantly slower folding kinetics formed much more stable complexes with SecB. In one case, we demonstrated that SecB did not need to be present cotranslationally for complex formation to occur. Formation of a complex between SecB and MBP was clearly not dependent on the MBP signal peptide. However, we were unable to detect complex formation between SecB and MBP lacking virtually the entire signal peptide but having a completely intact mature moiety. This MBP species folded at a rate considerably faster than that of wild-type preMBP. The propensity of this mutant protein to assume the native conformation of mature MBP apparently precludes a stable association with SecB, whereas an MBP species lacking a signal peptide but exhibiting altered folding properties did form a complex with SecB that could be precipitated with anti-SecB serum.
Expression of the Caulobacter heat shock gene dnaK is developmentally controlled during growth at normal temperatures
Authors: Gomes S L , Gober J W , Shapiro L
Published: November 2016

Caulobacter crescentus has a single dnaK gene that is highly homologous to the hsp70 family of heat shock genes. Analysis of the cloned and sequenced dnaK gene has shown that the deduced amino acid sequence could encode a protein of 67.6 kilodaltons that is 68% identical to the DnaK protein of Escherichia coli and 49% identical to the Drosophila and human hsp70 protein family. A partial open reading frame 165 base pairs 3' to the end of dnaK encodes a peptide of 190 amino acids that is 59% identical to DnaJ of E. coli. Northern blot analysis revealed a single 4.0-kilobase mRNA homologous to the cloned fragment. Since the dnaK coding region is 1.89 kilobases, dnaK and dnaJ may be transcribed as a polycistronic message. S1 mapping and primer extension experiments showed that transcription initiated at two sites 5' to the dnaK coding sequence. A single start site of transcription was identified during heat shock at 42 degrees C, and the predicted promoter sequence conformed to the consensus heat shock promoters of E. coli. At normal growth temperature (30 degrees C), a different start site was identified 3' to the heat shock start site that conformed to the E. coli sigma 70 promoter consensus sequence. S1 protection assays and analysis of expression of the dnaK gene fused to the lux transcription reporter gene showed that expression of dnaK is temporally controlled under normal physiological conditions and that transcription occurs just before the initiation of DNA replication. Thus, in both human cells (I. K. L. Milarski and R. I. Morimoto, Proc. Natl. Acad. Sci. USA 83:9517-9521, 1986) and in a simple bacterium, the transcription of a hsp70 gene is temporally controlled as a function of the cell cycle under normal growth conditions.
Role of the purine repressor in the regulation of pyrimidine gene expression in Escherichia coli K-12
Authors: Wilson H R , Turnbough C L
Published: November 2016

The pyrC and pyrD genes of Escherichia coli K-12 encode the pyrimidine biosynthetic enzymes dihydroorotase and dihydroorotate dehydrogenase, respectively. A highly conserved sequence in the promoter regions of these two genes is similar to the pur operator, which is the binding site for the purine repressor (PurR). In this study, we examined the role of PurR in the regulation of pyrC and pyrD expression. Our results show that pyrC and pyrD expression was repressed approximately twofold in cells grown in the presence of adenine [corrected] through a mechanism requiring PurR. A mutation, designated pyrCp926, which alters a 6-base-pair region within the conserved sequence in the pyrC promoter eliminated PurR-mediated repression of pyrC expression. This result indicates that PurR binds to the pyrC (and presumably to the pyrD) conserved sequence and inhibits transcriptional initiation. We also demonstrated that the pyrCp926 mutation had no effect on pyrimidine-mediated regulation of pyrC expression, indicating that pyrimidine and purine effectors act through independent mechanisms to control the expression of the pyrC and pyrD genes.
Cloning and sequencing of a gene encoding a glutamate and aspartate carrier of Escherichia coli K-12
Authors: Wallace B , Yang Y J , Hong J S , Lum D
Published: November 2016

A gene encoding a carrier protein for glutamate and aspartate was cloned into Escherichia coli K-12 strain BK9MDG by using the high-copy-number plasmid pBR322. The gene (designated gltP) is probably identical to a gene recently cloned from E. coli B (Y. Deguchi, I. Yamato, and Y. Anraku, J. Bacteriol. 171:1314-1319). A 1.6-kilobase DNA fragment containing gltP was subcloned into the expression plasmids pT7-5 and pT7-6, and its product was identified by a phage T7 RNA polymerase-T7 promoter coupled system (S. Tabor and C. C. Richardson, Proc. Natl. Acad. Sci. USA 82:1074-1078) as a polypeptide with an apparent mass of 38 kilodaltons. A portion of the gltP polypeptide was associated with the cytoplasmic membrane. The nucleotide sequence of the 1.6-kilobase fragment was determined. It contained an open reading frame capable of encoding a highly hydrophobic polypeptide of 395 amino acids, containing four possible transmembrane segments. Uptake of glutamate and aspartate was increased 5.5- and 4.5-fold, respectively, in strains containing gltP plasmids. Glutamate uptake was insensitive to the concentration of Na+ and was inhibited by L-cysteate and beta-hydroxyaspartate. These results suggest that gltP is a structural gene for a carrier protein of the Na(+)-independent, binding-protein-independent glutamate-aspartate transport system.
Roles of the two lysyl-tRNA synthetases of Escherichia coli: analysis of nucleotide sequences and mutant behavior
Authors: Clark R L , Neidhardt F C
Published: November 2016

The complete nucleotide sequence of lysU, the gene for the heat-inducible lysyl-tRNA synthetase of Escherichia coli, was determined and compared with the published sequence of lysS (herC), the gene for the constitutive lysyl-tRNA synthetase. These unlinked genes were found to be identical over 72% of their lengths. The deduced amino acid sequences of the respective gene products, LysU and LysS, were identical over 85% and similar over 92% of their lengths. Accumulation of high levels of LysU during growth of strains carrying the wild-type allele of lysU on multicopy plasmids had no observable effect on growth or on the synthesis of LysS. A lysU deletion strain was constructed and was shown to grow normally at low temperature (28 degrees C) but poorly at 44 degrees C; the slow growth (45% of normal) at elevated temperature was fully reversed by plasmids bearing wild-type lysU. The implications of these findings for the existence of two aminoacyl-tRNA synthetases for lysine are discussed.
The bof gene of bacteriophage P1: DNA sequence and evidence for roles in regulation of phage c1 and ref genes
Authors: Schaefer T S , Hays J B
Published: November 2016

The C1 repressor of bacteriophage P1 acts via 14 or more distinct operators. This repressor represses its own synthesis as well as the synthesis of other gene products. Previously, mutation of an auxiliary regulatory gene, bof, has been shown to increase expression of some C1-regulated P1 genes (e.g., ref) but to decrease expression of others (e.g., ban). In this study the bof gene was isolated on the basis of its ability to depress stimulation of Escherichia coli chromosomal recombination by the P1 ref gene, if and only if a source of C1 was present. C1 alone, but not Bof alone, was partially effective. The bofDNA sequence encodes an 82-codon reading frame that begins with a TTG codon and includes the sites of the bof-1(Am) mutation and a bof::Tn5 null mutation. Expression of ref::lacZ and cl::lacZ fusion genes was partially repressed in trans by a P1 bof-1 prophage or by plasmid-encoded C1 alone, which was in agreement with effects on Ref-stimulated recombination and with previous indirect evidence for c1 autoregulation. Repression of both fusion genes by plasmid-encoded C1 plus Bof or by a P1 bof+ prophage was more complete. When the C1 source also included a 0.7-kilobase region upstream from C1 which encodes the coi gene, repression of both c1::lacZ and ref::lacZ by C1 alone or by C1 plus Bof was much less effective, as if Coi interfered with C1 repressor function.
Cytosine methylation enhances Z-DNA formation in vivo
Authors: Zacharias W , Jaworski A , Wells R D
Published: November 2016

The influence of cytosine methylation on the supercoil-stabilized B-Z equilibrium in Escherichia coli was analyzed by two independent assays. Both the M.EcoRI inhibition assay and the linking-number assay have been used previously to establish that dC-dG segments of sufficient lengths can exist as left-handed helices in vivo. A series of dC-dG plasmid inserts with Z-form potential, ranging in length from 14 to 74 base pairs, was investigated. Complete methylation of cytosine at all HhaI sites, including the inserts, was obtained by coexpression of the HhaI methyltransferase (M.HhaI) in cells also carrying a dC-dG-containing plasmid. Both assays showed that for all lengths of dC-dG inserts, the relative amounts of B and Z helices were shifted to more Z-DNA in the presence of M.HhaI than in the absence of M.HhaI. These results indicate that cytosine methylation enhances the formation of Z-DNA helices at the superhelix density present in E. coli. The B-Z equilibrium, in combination with site-specific base methylation, may constitute a concerted mechanism for the modulation of DNA topology and DNA-protein interactions.
Sequence and structural characteristics of the trypsin-resistant T6 surface protein of group A streptococci
Authors: Schneewind O , Jones K F , Fischetti V A
Published: November 2016

The gene for the trypsin-resistant surface T6 protein of Streptococcus pyogenes D471 (M type 6) was cloned and expressed in Escherichia coli. The complete nucleotide sequence of the gene (tee6) and its flanking regions was determined and found to include only one major open reading frame coding for a protein of 537 amino acids (Mr, 57,675). The N terminus of the deduced protein sequence exhibits features of a typical signal sequence, and the C-terminal segment was found to have a high degree of homology with the membrane anchor region of other gram-positive surface proteins, such as streptococcal M protein, wapA protein from Streptococcus mutans and staphylococcal protein A. A hexapeptide having the consensus sequence LPSTGE and located immediately upstream of the C-terminal hydrophobic segment showed the highest degree of conservation at both the protein and DNA levels, with nearly all reported surface proteins from gram-positive cocci. The amino acid composition of the T6 protein revealed 21% serine and threonine residues distributed nearly regularly throughout the molecule, and analysis of the secondary structure predicted a conformation composed of greater than 70% beta-sheet potential interrupted by beta-turns or random coils. Localization experiments in E. coli show very little T6 protein in the periplasmic space. When found here, however, this T6 protein had a molecular mass of 55 kilodaltons, similar to that extracted from the streptococci by nonionic detergent. Most of the T6 protein was found localized in the membrane fraction, where it was composed of a triple band of 60, 58, and 57 kilodaltons. The coexistence of streptococcal surface proteins which are either resistant (T protein) or sensitive (M protein) to proteolytic enzymes may offer a new dimension to the modulation of these antigens under specific biological conditions.
Genes for two herbicide-inducible cytochromes P-450 from Streptomyces griseolus
Authors: Omer C A , Lenstra R , Litle P J , Dean C , Tepperman J M , Leto K J , Romesser J A , O'Keefe D P
Published: November 2016

Streptomyces griseolus ATCC 11796 contains two inducible, herbicide-metabolizing cytochromes P-450 previously designated P-450SU1 and P-450SU2 (P-450CVA1 and P-450CVB1, respectively, using nomenclature of Nebert et al. [D. W. Nebert, M. Adesnik, M. J. Coon, R. W. Estabrook, F. J. Gonzalez, F. P. Guengerich, I. C. Gunsalus, E. F. Johnson, B. Kemper, W. Levin, I. R. Phillips, R. Sato, and M. R. Waterman, DNA 6:1-11, 1987]). Using antibodies directed against cytochrome P-450SU1, its N-terminal amino acid sequence, and amino acid composition, we cloned the suaC gene encoding cytochrome P-450SU1. Similar information about the cytochrome P-450SU2 protein confirmed that a gene cloned by cross-hybridization to the suaC gene was the subC gene encoding cytochrome P-450SU2. The suaC and subC genes were expressed in Escherichia coli, DNA for both genes was sequenced, and the deduced amino acid sequences were compared with that of the well-characterized cytochrome P-450CAM from Pseudomonas putida. Both cytochromes P-450SU1 and P-450SU2 contain several regions of strong similarity with the amino acid sequence of P-450CAM, primarily in regions of the protein responsible for attachment and coordination of the heme prosthetic group.
Mutational analysis of the Shiga toxin and Shiga-like toxin II enzymatic subunits
Authors: Jackson M P , Deresiewicz R L , Calderwood S B
Published: November 2016

The A-subunit polypeptides of Shiga toxin, the Shiga-like toxins (SLTs), and the plant lectin ricin inactivate eucaryotic ribosomes by enzymatically depurinating 28S rRNA. Comparison of the amino acid sequences of the members of the Shiga toxin family and ricin revealed two regions of significant homology that lie within a proposed active-site cleft of the ricin A chain. In previous studies, these conserved sequences of the SLT-I and ricin A subunits have been implicated as active sites. To establish the importance of these regions of homology, we used site-directed mutagenesis to alter the A-subunit sequences of two members of the Shiga toxin family. Substitution of an aspartic acid for glutamic acid 166 of the Slt-IIA subunit decreased the capacity of the polypeptides to inhibit protein synthesis at least 100-fold in a cell-free translation system. However, this mutation did not prevent the expression of immunoreactive, full-length Slt-IIA. In addition, SLT-II holotoxin containing the mutated A subunit was 1,000-fold less toxic to Vero cells. Finally, site-directed mutagenesis was used to delete sequences encoding amino acids 202 through 213 of the Shiga toxin A subunit. Although this deletion did not prevent holotoxin assembly, it abolished cytotoxic activity.
Sulfate and thiosulfate transport in Escherichia coli K-12: nucleotide sequence and expression of the cysTWAM gene cluster
Authors: Sirko A , Hryniewicz M , Hulanicka D , Böck A
Published: November 2016

The nucleotide sequence of the sulfate and thiosulfate transport gene cluster has been determined and located 3' to the gene (cysP) encoding the thiosulfate-binding protein. Four open reading frames, designated cysT, cysW, cysA, and cysM, have been identified. Similarities in primary structure were observed between (i) the deduced amino acid sequences of CysT and CysW with membrane-bound components of other binding protein-dependent transport systems, (ii) that of the CysA sequence with the "conserved" component of such systems, and (iii) that of the CysM sequence with O-acetylserine sulfhydrylase A (cysK gene product) and the beta-subunit of tryptophan synthase (coded by trpB). Expression of the four genes was analyzed in the T7 promoter-polymerase system.
Membrane alteration is necessary but not sufficient for effective glutamate secretion in Corynebacterium glutamicum
Authors: Hoischen C , Krämer R
Published: November 2016

We showed recently that secretion of glutamate in biotin-limited cells of Corynebacterium glutamicum is mediated by carrier systems in the plasma membrane (C. Hoischen and R. Krämer, Arch. Microbiol. 151:342-347, 1989). In view of the generally accepted hypothesis that glutamate efflux is directly caused by alterations of the membrane, it was necessary to examine the kind of correlation between changes in lipid content and composition of the bacterial membrane and glutamate secretion activity. Two new experimental approaches were used. (i) Changes in lipid content and composition were analyzed in glutamate-producing cells which were forced to switch to nonproducers by addition of biotin in a short-term fermentation. (ii) The time courses of both the fatty acid or phospholipid composition and the efflux activity were analyzed within the first minutes of the switch from high to low secretion activity. The following results were obtained. (i) The time course of the change in fatty acid or phospholipid content and composition was not related to the change in secretion behavior. (ii) There was no specific fatty acid or phospholipid compound which regulated glutamate efflux. (iii) High efflux activity could only be induced when the total lipid content of the membrane was reduced. (iv) Although consistently correlated to high secretion activity, membrane alteration was never a sufficient prerequisite for glutamate efflux in C. glutamicum.
Studies of sigma D-dependent functions in Bacillus subtilis
Authors: Márquez L M , Helmann J D , Ferrari E , Parker H M , Ordal G W , Chamberlin M J
Published: November 2016

Gene expression in Bacillus subtilis can be controlled by alternative forms of RNA polymerase programmed by distinct sigma factors. One such factor, sigma D (sigma 28), is expressed during vegetative growth and has been implicated in the transcription of a regulon of genes expressed during exponential growth and the early stationary phase. We have studied several functions related to flagellar synthesis and chemotaxis in B. subtilis strains in which sigma D is missing or is present at reduced levels. Previous studies showed that a null mutant, which contains a disrupted copy of the sigma D structural gene (sigD), fails to synthesize flagellin and grows as long filaments. We now show that these defects are accompanied by the lack of synthesis of the methyl-accepting chemotaxis proteins and a substantial decrease in two autolysin activities implicated in cell separation. A strain containing an insertion upstream of the sigD gene that reduces the level of sigma D protein grew as short chains and was flagellated but was impaired in chemotaxis and/or motility. This reduced level of sigma D expression suggests that the sigD gene may be part of an operon. A strain containing an insertion downstream of the sigD gene expressed nearly wild-type levels of sigma D protein but was also impaired in chemotaxis and/or motility, suggesting that genes downstream of sigD may also be involved in these functions. Genetic experiments demonstrate that sigD is allelic to the flaB locus, which was initially isolated as a locus affecting flagellin expression (G. F. Grant and M. I. Simon, J. Bacteriol. 99:116-124, 1969).
Unique ribosome structure of Leptospira interrogans is composed of four rRNA components
Authors: Hsu D , Pan M J , Zee Y C , LeFebvre R B
Published: November 2016

All known ribosomes of procaryotic organisms are made up of three rRNA components that are 23, 16, and 5S in size. We now report that in some Leptospira interrogans strains, the classical 23S rRNA is further processed to generate 14 and 17S rRNAs. This processing step was previously known to occur only in some eucaryotes and in a small group of procaryotes. The implications of this finding are discussed.
Construction of broad-host-range plasmid vectors for easy visible selection and analysis of promoters
Authors: Farinha M A , Kropinski A M
Published: November 2016

We have constructed a series of broad-host-range plasmids which use "visual screens" to detect promoter activity. These plasmids contain the pMB1 and pRO1600 origins of replication and are capable of replicating in a wide range of gram-negative bacteria. The genes encoding beta-galactosidase and alkaline phosphatase from Escherichia coli and bacterial luciferase from Vibrio harveyi supply the promoterless indicator genes. The constructs were tested in E. coli and Pseudomonas aeruginosa.
Rule governing the division pattern in Escherichia coli minB and wild-type filaments
Authors: Jaffé A , Boye E , D'Ari R
Published: November 2016

Escherichia coli minB mutants form anucleate minicells and multinucleate filaments. We show here that the overwhelming majority of nucleate cells contain 2n (n = 0, 1, 2, ...) nucleoids, as determined by 4',6-diamidino-2-phenylindole staining, and 2n (n = 1, 2, 3, ...) copies of the replication origin, as determined by flow cytometry. This shows that division sites are not chosen randomly among the available sites in minB filaments. Similarly, wild-type cells contain 2n nucleoids, both during cell division inhibition and when furazlocillin-induced filaments are allowed to divide. We conclude that the min+ function is only to prevent septation only at polar sites; the placement of internal cell division sites must obey strict rules, which are the same in minB and wild-type cells.
Transduction of a plasmid containing the bacteriophage D3 cos site in Pseudomonas aeruginosa
Authors: Sharp R , Gertman E , Farinha M A , Kropinski A M
Published: November 2016

Plasmids harboring the cos sequences of bacteriophage D3 can be transferred, by bacteriophage D3, into Pseudomonas aeruginosa by a mechanism which is insensitive to DNase. Transducing activity was separated from the plaque-forming particles by CsCl equilibrium gradient centrifugation. Restriction endonuclease digestion patterns suggest that the transducing particles contain plasmid concatemers.
Characterization of biological ice nuclei from a lichen
Authors: Kieft T L , Ruscetti T
Published: November 2016

Biological ice nuclei (active at approximately -4 degrees C) were extracted from cells of the lichen Rhizoplaca chrysoleuca by sonication. Sensitivity to proteases, guanidine hydrochloride, and urea showed these nuclei to be proteinaceous. The nuclei were relatively heat stable, active from pH 1.5 to 12, and active without lipids, thereby demonstrating significant differences from bacterial ice nuclei.
Organization of the hao gene cluster of Nitrosomonas europaea: genes for two tetraheme c cytochromes
Authors: Bergmann D J , Arciero D M , Hooper A B
Published: November 2016

The organization of genes for three proteins involved in ammonia oxidation in Nitrosomonas europaea has been investigated. The amino acid sequence of the N-terminal region and four heme-containing peptides produced by proteolysis of the tetraheme cytochrome c554 of N. europaea were determined by Edman degradation. The gene (cycA) encoding this cytochrome is present in three copies per genome (H. McTavish, F. LaQuier, D. Arciero, M. Logan, G. Mundfrom, J.A. Fuchs, and A. B. Hooper, J. Bacteriol. 175:2445-2447, 1993). Three clones, representing at least two copies of cycA, were isolated and sequenced by the dideoxy-chain termination procedure. In both copies, the sequences of 211 amino acids derived from the gene sequence are identical and include all amino acids predicted by the proteolytic peptides. In two copies, the cycA open reading frame (ORF) is followed closely (three bases in one copy) by a second ORF predicted to encode a 28-kDa tetraheme c cytochrome not previously characterized but similar to the nirT gene product of Pseudomonas stutzeri. In one copy of the cycA gene cluster, the second ORF is absent.
Conjugation-independent, site-specific recombination at the oriT of the IncW plasmid R388 mediated by TrwC
Authors: Llosa M , Bolland S , Grandoso G , de la Cruz F
Published: November 2016

Plasmids containing a direct repeat of plasmid R388 oriT are capable of site-specific recombination, which results in deletion of the intervening DNA. This reaction occurs in the presence, but not in the absence, of the region of R388 implicated in DNA processing during conjugation. This region contains three genes, trwA, trwB, and trwC. By using mutants of each of the three genes, it was demonstrated that only trwC is required for the oriT-specific recombination. Further analysis showed that the N-terminal 272 amino acids of the protein are sufficient to catalyze recombination. TrwC is also capable of promoting intermolecular recombination between two plasmids containing oriT, suggesting that double-strand breaks in both plasmid DNAs are involved in the process. Additionally, intramolecular recombination between R388 oriT and R46 oriT did not occur in the presence of both nickases. This suggests that the half-reactions at each oriT are not productive if they occur separately; therefore, an interaction between the recombination complexes formed at each recombining site is required. This is the first report in which a nicking-closing enzyme involved in conjugal DNA transfer promotes oriT-specific recombination of double-stranded DNA in the absence of conjugation.
Pullulanase of Thermoanaerobacterium thermosulfurigenes EM1 (Clostridium thermosulfurogenes): molecular analysis of the gene, composite structure of the enzyme, and a common model for its attachment to the cell surface
Authors: Matuschek M , Burchhardt G , Sahm K , Bahl H
Published: November 2016

The complete pullulanase gene (amyB) from Thermoanaerobacterium thermosulfurigenes EM1 was cloned in Escherichia coli, and the nucleotide sequence was determined. The reading frame of amyB consisted of 5,586 bp encoding an exceptionally large enzyme of 205,991 Da. Sequence analysis revealed a composite structure of the pullulanase consisting of catalytic and noncatalytic domains. The N-terminal half of the protein contained a leader peptide of 35 amino acid residues and the catalytic domain, which included the four consensus regions of amylases. Comparison of the consensus regions of several pullulanases suggested that enzymes like pullulanase type II from T. thermosulfurigenes EM1 which hydrolyze alpha-1,4- and alpha-1,6-glycosidic linkages have specific amino acid sequences in the consensus regions. These are different from those of pullulanases type I which only cleave alpha-1,6 linkages. The C-terminal half, which is not necessary for enzymatic function, consisted of at least two different segments. One segment of about 70 kDa contained two copies of a fibronectin type III-like domain and was followed by a linker region rich in glycine, serine, and threonine residues. At the C terminus, we found three repeats of about 50 amino acids which are also present at the N-termini of surface layer (S-layer) proteins of, e.g., Thermus thermophilus and Acetogenium kivui. Since the pullulanase of T. thermosulfurigenes EM1 is known to be cell bound, our results suggest that this segment serves as an S-layer anchor to keep the pullulanase attached to the cell surface. Thus, a general model for the attachment of extracellular enzymes to the cell surface is proposed which assigns the S-layer a new function and might be widespread among bacteria with S-layers. The triplicated S-layer-like segment is present in several enzymes of different bacteria. Upstream of amyB, another open reading frame, coding for a hypothetical protein of 35.6 kDa, was identified. No significant similarity to other sequences available in DNA and protein data bases was found.