bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcription of theSalmonellaInvasion Gene Activator,hilA, Requires HilD Activation in the Absence of Negative Regulators
Authors: Boddicker Jennifer D. , Knosp Boyd M. , Jones Bradley D. 
Published: January 2003

ABSTRACTSalmonella entericaserovar Typhimurium causes human gastroenteritis and a systemic typhoid-like infection in mice. Infection is initiated by entry of the bacteria into intestinal epithelial cells and is mediated by a type III secretion system that is encoded by genes inSalmonellapathogenicity island 1. The expression of invasion genes is tightly regulated by environmental conditions such as oxygen and osmolarity, as well as by many bacterial factors. ThehilAgene encodes an OmpR/ToxR family transcriptional regulator that activates the expression of invasion genes in response to both environmental and genetic regulatory factors. HilD is an AraC/XylS regulator that has been postulated to act as a derepressor ofhilAexpression that promotes transcription by interfering with repressor binding at thehilApromoter. Our research group has identified four genes (hilE,hha,pag, andams) that negatively affecthilAtranscription. Since the postulated function of HilD at thehilApromoter is to counteract the effects of repressors, we examined this model by measuringhilA::Tn5lacZYexpression in strains containing negative regulator mutations in the presence or absence of functional HilD. Single negative regulator mutations caused significant derepression ofhilAexpression, and two or more negative regulator mutations led to very high level expression ofhilA. However, in all strains tested, the absence ofhilDresulted in low-level expression ofhilA, suggesting that HilD is required for activation ofhilAexpression, whether or not negative regulators are present. We also observed that deletion of the HilD binding sites in the chromosomalhilApromoter severely decreasedhilAexpression. In addition, we found that a single point mutation at leucine 289 in the C-terminal domain of the α subunit of RNA polymerase leads to very low levels ofhilA::Tn5lacZYexpression, suggesting that HilD activates transcription ofhilAby contacting and recruiting RNA polymerase to thehilApromoter.
Different Evolutionary Constraints on Chemotaxis Proteins CheW and CheY Revealed by Heterologous Expression Studies and Protein Sequence Analysis
Authors: Alexandre Gladys , Zhulin Igor B. 
Published: January 2003

ABSTRACT

CheW and CheY are single-domain proteins from a signal transduction pathway that transmits information from transmembrane receptors to flagellar motors in bacterial chemotaxis. In various bacterial and archaeal species, the
cheW
and
cheY
genes are usually encoded within homologous chemotaxis operons. We examined evolutionary changes in these two proteins from distantly related proteobacterial species,
Escherichia coli
and
Azospirillum brasilense
. We analyzed the functions of divergent CheW and CheY proteins from
A. brasilense
by heterologous expression in
E. coli
wild-type and mutant strains. Both proteins were able to specifically inhibit chemotaxis of a wild-type
E. coli
strain; however, only CheW from
A. brasilense
was able to restore signal transduction in a corresponding mutant of
E. coli
. Detailed protein sequence analysis of CheW and CheY homologs from the two species revealed substantial differences in the types of amino acid substitutions in the two proteins. Multiple, but conservative, substitutions were found in CheW homologs. No severe mismatches were found between the CheW homologs in positions that are known to be structurally or functionally important. Substitutions in CheY homologs were found to be less conservative and occurred in positions that are critical for interactions with other components of the signal transduction pathway. Our findings suggest that proteins from the same cellular pathway encoded by genes from the same operon have different evolutionary constraints on their structures that reflect differences in their functions.
Genomic Comparison of
Salmonella enterica
Serovars and
Salmonella bongori
by Use of an
S. enterica
Serovar Typhimurium DNA Microarray
Authors: Chan Kaman , Baker Stephen , Kim Charles C. , Detweiler Corrella S. , Dougan Gordon , Falkow Stanley 
Published: January 2003

ABSTRACT

The genus
Salmonella
consists of over 2,200 serovars that differ in their host range and ability to cause disease despite their close genetic relatedness. The genetic factors that influence each serovar's level of host adaptation, how they evolved or were acquired, their influence on the evolution of each serovar, and the phylogenic relationships between the serovars are of great interest as they provide insight into the mechanisms behind these differences in host range and disease progression. We have used an
Salmonella enterica
serovar Typhimurium spotted DNA microarray to perform genomic hybridizations of various serovars and strains of both
S. enterica
(subspecies I and IIIa) and
Salmonella bongori
to gain insight into the genetic organization of the serovars. Our results are generally consistent with previously published DNA association and multilocus enzyme electrophoresis data. Our findings also reveal novel information. We observe a more distant relationship of serovar Arizona (subspecies IIIa) from the subspecies I serovars than previously measured. We also observe variability in the Arizona SPI-2 pathogenicity island, indicating that it has evolved in a manner distinct from the other serovars. In addition, we identify shared genetic features of
S. enterica
serovars Typhi, Paratyphi A, and Sendai that parallel their unique ability to cause enteric fever in humans. Therefore, whereas the taxonomic organization of
Salmonella
into serogroups provides a good first approximation of genetic relatedness, we show that it does not account for genomic changes that contribute to a serovar's degree of host adaptation.
Microcystin Biosynthesis in
Planktothrix
: Genes, Evolution, and Manipulation
Authors: Christiansen Guntram , Fastner Jutta , Erhard Marcel , Börner Thomas , Dittmann Elke 
Published: January 2003

ABSTRACT

Microcystins represent an extraordinarily large family of cyclic heptapeptide toxins that are nonribosomally synthesized by various cyanobacteria. Microcystins specifically inhibit the eukaryotic protein phosphatases 1 and 2A. Their outstanding variability makes them particularly useful for studies on the evolution of structure-function relationships in peptide synthetases and their genes. Analyses of microcystin synthetase genes provide valuable clues for the potential and limits of combinatorial biosynthesis. We have sequenced and analyzed 55.6 kb of the potential microcystin synthetase gene (
mcy
) cluster from the filamentous cyanobacterium
Planktothrix agardhii
CYA 126. The cluster contains genes for peptide synthetases (
mcyABC
), polyketide synthases (PKSs;
mcyD
), chimeric enzymes composed of peptide synthetase and PKS modules (
mcyEG
), a putative thioesterase (
mcyT
), a putative ABC transporter (
mcyH
), and a putative peptide-modifying enzyme (
mcyJ
). The gene content and arrangement and the sequence of specific domains in the gene products differ from those of the
mcy
cluster in
Microcystis
, a unicellular cyanobacterium. The data suggest an evolution of
mcy
clusters from, rather than to, genes for nodularin (a related pentapeptide) biosynthesis. Our data do not support the idea of horizontal gene transfer of complete
mcy
gene clusters between the genera. We have established a protocol for stable genetic transformation of
Planktothrix
, a genus that is characterized by multicellular filaments exhibiting continuous motility. Targeted mutation of
mcyJ
revealed its function as a gene coding for a
O
-methyltransferase. The mutant cells produce a novel microcystin variant exhibiting reduced inhibitory activity toward protein phosphatases.
Enhanced Expression ofS-Adenosylmethionine Synthetase Causes Overproduction of Actinorhodin inStreptomyces coelicolorA3(2)
Authors: Okamoto Susumu , Lezhava Alexander , Hosaka Takeshi , Okamoto-Hosoya Yoshiko , Ochi Kozo 
Published: January 2003

ABSTRACTWe found that a 46-kDa protein is highly expressed in an actinorhodin-overproducingStreptomyces coelicolorA3(2) mutant (KO-179), which exhibited a low-level resistance to streptomycin. The protein was identified asS-adenosylmethionine (SAM) synthetase, which is a product of themetKgene. Enzyme assay revealed that SAM synthetase activity in strain KO-179 was 5- to 10-fold higher than in wild-type cells. The elevation of SAM synthetase activity was found to be associated with an increase in the level of intracellular SAM. RNase protection assay revealed that themetKgene was transcribed from two distinct promoters (p1 and p2) and that enhanced expression of the MetK protein in the mutant strain KO-179 was attributed to elevated transcription frommetKp2. Strikingly, the introduction of a high-copy-number plasmid containing themetKgene into wild-type cells resulted in a precocious hyperproduction of actinorhodin. Furthermore, the addition of SAM to the culture medium induced Act biosynthesis in wild-type cells. Overexpression ofmetKstimulated the expression of the pathway-specific regulatory geneactII-ORF4, as demonstrated by the RNase protection assay. The addition of SAM also caused hyperproduction of streptomycin inStreptomyces griseus. These findings implicate the significant involvement of intracellular SAM in initiating the onset of secondary metabolism inStreptomyces.
Development of Methicillin Resistance in Clinical Isolates of
Staphylococcus sciuri
by Transcriptional Activation of the
mecA
Homologue Native to the Species
Authors: Couto Isabel , Wu Shang Wei , Tomasz Alexander , de Lencastre Hermínia 
Published: January 2003

ABSTRACT

The β-lactam resistance gene
mecA
was acquired by
Staphylococcus aureus
from an extraspecies source. The search for the possible origin of this gene has led to the identification of a close structural homologue of
mecA
as a native gene in the animal species
Staphylococcus sciuri.
Surprisingly, the overwhelming majority of
S. sciuri
isolates were fully susceptible to β-lactam antibiotics in spite of the ubiquitous presence of the
mecA
homologue in the bacteria. We now describe two unusual
S. sciuri
strains isolated from humans—SS-37 and SS-41—that showed resistance to methicillin associated with high rates of transcription of the
mecA
homologue and production of a protein resembling penicillin binding protein 2a, the gene product of
S. aureus mecA
. In strain SS-37 increased transcription of the
mecA
homologue was related to insertion of an IS
256
element upstream of the structural gene, and strain SS-41 had single nucleotide alterations in the promoter region of the
mecA
homologue which appear to be related to up-regulation of the rate of transcription. A third methicillin-resistant human isolate of
S. sciuri
that carries both the native
mecA
homologue and a methicillin-resistant
S. aureus
(MRSA) type
mecA
, strain K3, was now shown to be unstable in the absence of drug selection, causing the segregation of antibiotic-susceptible cells accompanied by the loss of the MRSA type
mecA
. These observations illustrate the remarkable variety of strategies available to bacteria for acquiring mechanisms of drug resistance in the in vivo environment.
Formation of an F′ Plasmid by Recombination between Imperfectly Repeated Chromosomal Rep Sequences: a Closer Look at an Old Friend (F′
128
pro lac
)
Authors: Kofoid Eric , Bergthorsson Ulfar , Slechta E. Susan , Roth John R. 
Published: January 2003

ABSTRACT

Plasmid F′
128
was formed by an exchange between chromosomal Rep sequences that placed
lac
near
dinB
between many pairs of Rep sequences. Plasmid F′
128
is critical for selection-enhanced
lac
reversion (adaptive mutation), which requires prior
lac
amplification. The structure of F′
128
supports the idea that amplification is initiated by Rep-Rep recombination and that general mutagenesis requires coamplification of
dinB
(error-prone polymerase) with
lac
.
Flagella and Motility inActinobacillus pleuropneumoniae
Authors: Negrete-Abascal Erasmo , Reyes Magda E. , García Rosa M. , Vaca Sergio , Girón Jorge A. , García Octavio , Zenteno Edgar , de la Garza Mireya 
Published: January 2003

ABSTRACTActinobacillus pleuropneumoniaehas been considered nonmotile and nonflagellate. In this work, it is demonstrated thatA. pleuropneumoniaeproduces flagella composed of a 65-kDa protein with an N-terminal amino acid sequence that shows 100% identity with those ofEscherichia coli,Salmonella, andShigellaflagellins. The DNA sequence obtained through PCR of thefliCgene inA. pleuropneumoniaeshowed considerable identity (93%) in its 5′ and 3′ ends with the DNA sequences of corresponding genes inE. coli,Salmonella enterica, andShigellaspp. The motility ofA. pleuropneumoniaewas observed in tryptic soy or brain heart infusion soft agar media, and it is influenced by temperature. Flagella and motility may be involved in the survival and pathogenesis ofA. pleuropneumoniaein pigs.
Signal Transduction Cascades Regulating Fungal Development and Virulence
Authors: Lengeler Klaus B. , Davidson Robert C. , D'souza Cletus , Harashima Toshiaki , Shen Wei-Chiang , Wang Ping , Pan Xuewen , Waugh Michael , Heitman Joseph 
Published: January 2003

SUMMARY
Cellular differentiation, mating, and filamentous growth are regulated in many fungi by environmental and nutritional signals. For example, in response to nitrogen limitation, diploid cells of the yeast Saccharomyces cerevisiae undergo a dimorphic transition to filamentous growth referred to as pseudohyphal differentiation. Yeast filamentous growth is regulated, in part, by two conserved signal transduction cascades: a mitogen-activated protein kinase cascade and a G-protein regulated cyclic AMP signaling pathway. Related signaling cascades play an analogous role in regulating mating and virulence in the plant fungal pathogen Ustilago maydis and the human fungal pathogens Cryptococcus neoformans and Candida albicans. We review here studies on the signaling cascades that regulate development of these and other fungi. This analysis illustrates both how the model yeast S. cerevisiae can serve as a paradigm for signaling in other organisms and also how studies in other fungi provide insights into conserved signaling pathways that operate in many divergent organisms.
Hyperthermophilic Enzymes: Sources, Uses, and Molecular Mechanisms for Thermostability
Authors: Vieille Claire , Zeikus Gregory J. 
Published: January 2003

SUMMARYEnzymes synthesized by hyperthermophiles (bacteria and archaea with optimal growth temperatures of >80°C), also called hyperthermophilic enzymes, are typically thermostable (i.e., resistant to irreversible inactivation at high temperatures) and are optimally active at high temperatures. These enzymes share the same catalytic mechanisms with their mesophilic counterparts. When cloned and expressed in mesophilic hosts, hyperthermophilic enzymes usually retain their thermal properties, indicating that these properties are genetically encoded. Sequence alignments, amino acid content comparisons, crystal structure comparisons, and mutagenesis experiments indicate that hyperthermophilic enzymes are, indeed, very similar to their mesophilic homologues. No single mechanism is responsible for the remarkable stability of hyperthermophilic enzymes. Increased thermostability must be found, instead, in a small number of highly specific alterations that often do not obey any obvious traffic rules. After briefly discussing the diversity of hyperthermophilic organisms, this review concentrates on the remarkable thermostability of their enzymes. The biochemical and molecular properties of hyperthermophilic enzymes are described. Mechanisms responsible for protein inactivation are reviewed. The molecular mechanisms involved in protein thermostabilization are discussed, including ion pairs, hydrogen bonds, hydrophobic interactions, disulfide bridges, packing, decrease of the entropy of unfolding, and intersubunit interactions. Finally, current uses and potential applications of thermophilic and hyperthermophilic enzymes as research reagents and as catalysts for industrial processes are described.
Biosynthesis of Polyketides in Heterologous Hosts
Authors: Pfeifer Blaine A. , Khosla Chaitan 
Published: January 2003

SUMMARY
Polyketide natural products show great promise as medicinal agents. Typically the products of microbial secondary biosynthesis, polyketides are synthesized by an evolutionarily related but architecturally diverse family of multifunctional enzymes called polyketide synthases. A principal limitation for fundamental biochemical studies of these modular megasynthases, as well as for their applications in biotechnology, is the challenge associated with manipulating the natural microorganism that produces a polyketide of interest. To ameliorate this limitation, over the past decade several genetically amenable microbes have been developed as heterologous hosts for polyketide biosynthesis. Here we review the state of the art as well as the difficulties associated with heterologous polyketide production. In particular, we focus on two model hosts, Streptomyces coelicolor and Escherichia coli. Future directions for this relatively new but growing technological opportunity are also discussed.
Transition between Stochastic Evolution and Deterministic Evolution in the Presence of Selection: General Theory and Application to Virology
Authors: Rouzine I. M. , Rodrigo A. , Coffin J. M. 
Published: January 2003

SUMMARYWe present here a self-contained analytic review of the role of stochastic factors acting on a virus population. We develop a simple one-locus, two-allele model of a haploid population of constant size including the factors of random drift, purifying selection, and random mutation. We consider different virological experiments: accumulation and reversion of deleterious mutations, competition between mutant and wild-type viruses, gene fixation, mutation frequencies at the steady state, divergence of two populations split from one population, and genetic turnover within a single population. In the first part of the review, we present all principal results in qualitative terms and illustrate them with examples obtained by computer simulation. In the second part, we derive the results formally from a diffusion equation of the Wright-Fisher type and boundary conditions, all derived from the first principles for the virus population model. We show that the leading factors and observable behavior of evolution differ significantly in three broad intervals of population size, N. The “neutral limit” is reached when N is smaller than the inverse selection coefficient. When N is larger than the inverse mutation rate per base, selection dominates and evolution is “almost” deterministic. If the selection coefficient is much larger than the mutation rate, there exists a broad interval of population sizes, in which weakly diverse populations are almost neutral while highly diverse populations are controlled by selection pressure. We discuss in detail the application of our results to human immunodeficiency virus population in vivo, sampling effects, and limitations of the model.
Viruses in the Mammalian Male Genital Tract and Their Effects on the Reproductive System
Authors: Dejucq Nathalie , Jégou Bernard 
Published: January 2003

SUMMARYThis review describes the various viruses identified in the semen and reproductive tracts of mammals (including humans), their distribution in tissues and fluids, their possible cell targets, and the functional consequences of their infectivity on the reproductive and endocrine systems. The consequences of these viral infections on the reproductive tract and semen can be extremely serious in terms of organ integrity, development of pathological and cancerous processes, and transmission of diseases. Furthermore, of essential importance is the fact that viral infection of the testicular cells may result not only in changes in testicular function, a serious risk for the fertility and general health of the individual (such as a fall in testosteronemia leading to cachexia), but also in the possible transmission of virus-induced mutations to subsequent generations. In addition to providing an exhaustive account of the data available in these domains, this review focuses attention on the fact that the interface between endocrinology and virology has so far been poorly explored, particularly when major health, social and economical problems are posed. Our conclusions highlight the research strategies that need to be developed. Progress in all these domains is essential for the development of new treatment strategies to eradicate viruses and to correct the virus-induced dysfunction of the endocrine system.
Natural Biology of Polyomavirus Middle T Antigen
Authors: Gottlieb Keith A. , Villarreal Luis P. 
Published: January 2003

SUMMARY“It has been commented by someone that ‘polyoma’ is an adjective composed of a prefix and suffix, with no root between—a meatless linguistic sandwich” (C. J. Dawe). The very name “polyomavirus” is a vague mantel: a name given before our understanding of these viral agents was clear but implying a clear tumor life-style, as noted by the late C. J. Dawe. However, polyomavirus are not by nature tumor-inducing agents. Since it is the purpose of this review to consider the natural function of middle T antigen (MT), encoded by one of the seemingly crucial transforming genes of polyomavirus, we will reconsider and redefine the virus and its MT gene in the context of its natural biology and function. This review was motivated by our recent in vivo analysis of MT function. Using intranasal inoculation of adult SCID mice, we have shown that polyomavirus can replicate with an MT lacking all functions associated with transformation to similar levels to wild-type virus. These observations, along with an almost indistinguishable replication of all MT mutants with respect to wild-type viruses in adult competent mice, illustrate that MT can have a play subtle role in acute replication and persistence. The most notable effect of MT mutants was in infections of newborns, indicating that polyomavirus may be highly adapted to replication in newborn lungs. It is from this context that our current understanding of this well-studied virus and gene is presented.