bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary Genetics of the Capsular Locus of Serogroup 6 Pneumococci
Authors: Mavroidi Angeliki , Godoy Daniel , Aanensen David M. , Robinson D. Ashley , Hollingshead Susan K. , Spratt Brian G. 
Published: December 2004

ABSTRACT

The evolution of the capsular biosynthetic (
cps
) locus of serogroup 6
Streptococcus pneumoniae
was investigated by analyzing sequence variation within three serotype-specific
cps
genes from 102 serotype 6A and 6B isolates. Sequence variation within these
cps
genes was related to the genetic relatedness of the isolates, determined by multilocus sequence typing, and to the inferred patterns of recent evolutionary descent, explored using the eBURST algorithm. The serotype-specific
cps
genes had a low percent G+C, and there was a low level of sequence diversity in this region among serotype 6A and 6B isolates. There was also little sequence divergence between these serotypes, suggesting a single introduction of an ancestral
cps
sequence, followed by slight divergence to create serotypes 6A and 6B. A minority of serotype 6B isolates had
cps
sequences (class 2 sequences) that were ∼5% divergent from those of other serotype 6B isolates (class 1 sequences) and which may have arisen by a second, more recent introduction from a related but distinct source. Expression of a serotype 6A or 6B capsule correlated perfectly with a single nonsynonymous polymorphism within
wciP
, the rhamnosyl transferase gene. In addition to ample evidence of the horizontal transfer of the serotype 6A and 6B
cps
locus into unrelated lineages, there was evidence for relatively frequent changes from serotype 6A to 6B, and vice versa, among very closely related isolates and examples of recent recombinational events between class 1 and 2
cps
serogroup 6 sequences.
Characterization of LytA-LikeN-Acetylmuramoyl-l-Alanine Amidases from Two NewStreptococcus mitisBacteriophages Provides Insights into the Properties of the Major Pneumococcal Autolysin
Authors: Romero Patricia , López Rubens , García Ernesto 
Published: December 2004

ABSTRACTTwo new temperate bacteriophages exhibiting aMyoviridae(φB6) and aSiphoviridae(φHER) morphology have been isolated fromStreptococcus mitisstrains B6 and HER 1055, respectively, and partially characterized. The lytic phage genes were overexpressed inEscherichia coli, and their encoded proteins were purified. ThelytAHERandlytAB6genes are very similar (87% identity) and appeared to belong to the group of the so-called typical LytA amidases (atypical LytA displays a characteristic two-amino-acid deletion signature). although they exhibited several differential biochemical properties with respect to the pneumococcal LytA, e.g., they were inhibited in vitro by sodium deoxycholate and showed a more acidic pH for optimal activity. However, and in sharp contrast with the pneumococcal LytA, a short dialysis of LytAHERor LytAB6resulted in reversible deconversion to the low-activity state (E-form) of the fully active phage amidases (C-form). Comparison of the amino acid sequences of LytAHERand LytAB6with that of the pneumococcal amidase suggested that Val317might be responsible for at least some of the peculiar properties ofS. mitisphage enzymes. Site-directed mutagenesis that changed Val317in the pneumococcal LytA amidase to a Thr residue (characteristic of LytAB6and LytAHER) produced a fully active pneumococcal enzyme that differs from the parental one only in that the mutant amidase can reversibly recover the low-activity E-form upon dialysis. This is the first report showing that a single amino acid residue is involved in the conversion process of the majorS. pneumoniaeautolysin. Our results also showed that some lysogenicS. mitisstrains possess alytA-like gene, something that was previously thought to be exclusive toStreptococcus pneumoniae. Moreover, the newly discovered phage lysins constitute a missing link between the typical and atypical pneumococcal amidases known previously.
Comparative Sequence Analysis of IS50/Tn5Transposase
Authors: Reznikoff William S. , Bordenstein Seth R. , Apodaca Jennifer 
Published: December 2004

ABSTRACTComparative sequence analysis of IS50transposase-related protein sequences in conjunction with known structural, biochemical, and genetic data was used to determine domains and residues that play key roles in IS50transposase function. BLAST and ClustalW analyses have been used to find and analyze six complete protein sequences that are related to the IS50transposase. The protein sequence identity of these six homologs ranged from 25 to 55% in comparison to the IS50transposase. Homologous motifs were found associated with each of the three catalytic residues. Residues that play roles in transposase-DNA binding, protein autoregulation, and DNA hairpin formation were also found to be conserved in addition to other residues of unknown function. On the other hand, some homologous sequences did not appear to be competent to encode the inhibitor regulatory protein. The results were also used to compare the IS50transposase with the more distantly related transposase encoded by IS10.
Identification of the
Escherichia coli
K-12
ybhE
Gene as
pgl
, Encoding 6-Phosphogluconolactonase
Authors: Thomason Lynn C. , Court Donald L. , Datta Atin R. , Khanna Rita , Rosner Judah L. 
Published: December 2004

ABSTRACT

We report identification of the
Escherichia coli ybhE
gene as the
pgl
gene that encodes 6-phosphogluconolactonase. A tentative identification was first made based on the known approximate location of the
pgl
gene and the similarity of the presumptive ybhE-encoded protein sequence to a known Pgl enzyme. To test this notion, the
ybhE
gene was deleted and replaced with a drug marker. Like previously characterized
pgl
mutants, the
ybhE
deletion mutant had a Blu
−
phenotype (dark-blue staining with iodine due to accumulation of starch after growth on minimal maltose) and demonstrated impaired growth on minimal glucose medium when combined with a
pgi
mutation. Biochemical assay of crude extracts for 6-phosphogluconolactonase enzymatic activity showed that
ybhE
encodes this activity. The
ybhE
gene was transferred from the
E. coli
chromosome to an expression vector. This
ybhE
clone complemented both the precise deletion of the
ybhE
gene and a larger deletion,
pgl
Δ
8
, for the Blu
−
phenotype and for phosphogluconolactonase activity, confirming that
ybhE
is the
pgl
gene. A newly observed phenotype of
pgl
strains is a lowered frequency of appearance of Bgl
+
mutants that can utilize the β-glucoside salicin. This is likely due to poor growth of Bgl
+
pgl
strains on salicin due to the accumulation of 6-phosphogluconolactone.
In Vivo Bypass of Chaperone by Extended Coiled-Coil Motif in T4 Tail Fiber
Authors: Qu Yun , Hyman Paul , Harrah Timothy , Goldberg Edward 
Published: December 2004

ABSTRACT

The distal-half tail fiber of bacteriophage T4 is made of three gene products: trimeric gp36 and gp37 and monomeric gp35. Chaperone P38 is normally required for folding gp37 peptides into a P37 trimer; however, a temperature-sensitive mutation in T4 (ts3813) that suppresses this requirement at 30°C but not at 42°C was found in gene 37 (R. J. Bishop and W. B. Wood, Virology
72:
244-254, 1976). Sequencing of the temperature-sensitive mutant revealed a 21-bp duplication of wild-type gene 37 inserted into its C-terminal portion (S. Hashemolhosseini et al., J. Mol. Biol.
241:
524-533, 1994). We noticed that the 21-amino-acid segment encompassing this duplication in the ts3813 mutant has a sequence typical of a coiled coil and hypothesized that its extension would relieve the temperature sensitivity of the ts3813 mutation. To test our hypothesis, we crossed the T4 ts3813 mutant with a plasmid encoding an engineered pentaheptad coiled coil. Each of the six mutants that we examined retained two amber mutations in gene 38 and had a different coiled-coil sequence varying from three to five heptads. While the sequences varied, all maintained the heptad-repeating coiled-coil motif and produced plaques at up to 50°C. This finding strongly suggests that the coiled-coil motif is a critical factor in the folding of gp37. The presence of a terminal coiled-coil-like sequence in the tail fiber genes of 17 additional T-even phages implies the conservation of this mechanism. The increased melting temperature should be useful for “clamps” to initiate the folding of trimeric β-helices in vitro and as an in vivo screen to identify, sequence, and characterize trimeric coiled coils.
Phage φ29 Proteins p1 and p17 Are Required for Efficient Binding of Architectural Protein p6 to Viral DNA In Vivo
Authors: González-Huici Víctor , Alcorlo Martín , Salas Margarita , Hermoso José M. 
Published: December 2004

ABSTRACT

Bacteriophage φ29 protein p6 is a viral architectural protein, which binds along the whole linear φ29 DNA in vivo and is involved in initiation of DNA replication and transcription control. Protein p1 is a membrane-associated viral protein, proposed to attach the viral genome to the cell membrane. Protein p17 is involved in pulling φ29 DNA into the cell during the injection process. We have used chromatin immunoprecipitation and real-time PCR to analyze in vivo p6 binding to DNA in cells infected with φ29
sus1
or
sus17
mutants; in both cases p6 binding is significantly decreased all along φ29 DNA. φ29 DNA is topologically constrained in vivo, and p6 binding is highly increased in the presence of novobiocin, a gyrase inhibitor that produces a loss of DNA negative superhelicity. Here we show that, in cells infected with φ29
sus1
or
sus17
mutants, the increase of p6 binding by novobiocin is even higher than in cells containing p1 and p17, alleviating the p6 binding deficiency. Therefore, proteins p1 and p17 could be required to restrain the proper topology of φ29 DNA, which would explain the impaired DNA replication observed in cells infected with
sus1
or
sus17
mutants.
The RpoH-Mediated Stress Response in
Neisseria gonorrhoeae
Is Regulated at the Level of Activity
Authors: Laskos Lina , Ryan Catherine S. , Fyfe Janet A. M. , Davies John K. 
Published: December 2004

ABSTRACT

The general stress response in
Neisseria gonorrhoeae
was investigated. Transcriptional analyses of the genes encoding the molecular chaperones DnaK, DnaJ, and GrpE suggested that they are transcribed from σ
32
(RpoH)-dependent promoters upon exposure to stress. This was confirmed by mutational analysis of the σ
32
promoter of
dnaK
. The gene encoding the gonococcal RpoH sigma factor appears to be essential, as we could not isolate viable mutants. Deletion of an unusually long
rpoH
leader sequence resulted in elevated levels of transcription, suggesting that this region is involved in negative regulation of RpoH expression during normal growth. Transcriptional analyses and protein studies determined that regulation of the RpoH-mediated stress response is different from that observed in most other species, in which regulation occurs predominantly at the transcriptional and translational levels. We suggest that an increase in the activity of preformed RpoH is primarily responsible for induction of the stress response in
N. gonorrhoeae
.
Revising the Role of the Pneumococcalvex-vncRSLocus in Vancomycin Tolerance
Authors: Haas Wolfgang , Sublett Jack , Kaushal Deepak , Tuomanen Elaine I. 
Published: December 2004

ABSTRACTVancomycin is used increasingly to treat invasive infections caused by multidrug-resistantStreptococcus pneumoniae. Although no vancomycin-resistant strains have been isolated to date, tolerant strains that fail to die rapidly and that cause relapsing disease have been described. Thevex123-pep27-vncRSlocus, consisting of an ABC transporter, a presumed signaling peptide, and a two-component system, respectively, has been implicated in vancomycin tolerance. Recent findings, however, challenged this model. The data presented here indicate that erythromycin in the growth medium induces a vancomycin-tolerant phenotype and that loss of function of Pep27or VncRS does not alter autolysis. However, a role for the ABC transporter encoded by thevex123genes in tolerance was confirmed. Avex3mutant was considerably more tolerant to vancomycin treatment than the wild-type strain T4, and the strength of the phenotype depended on the orientation of the resistance cassette used to construct the mutant. Microarray results suggested a number of genes that might be involved in tolerance in thevex3mutant. Although the exact function and regulation of thevex123-pep27-vncRSlocus remains to be determined, several factors influence the autolysis behavior ofS. pneumoniae, including the bacterial capsule, erythromycin, and thelytAandvex3gene products.
The Etiological Agent of Lyme Disease,Borrelia burgdorferi, Appears To Contain Only a Few Small RNA Molecules
Authors: Östberg Yngve , Bunikis Ignas , Bergström Sven , Johansson Jörgen 
Published: December 2004

ABSTRACTSmall regulatory RNAs (sRNAs) have recently been shown to be the main controllers of several regulatory pathways. The function of sRNAs depends in many cases on the RNA-binding protein Hfq, especially for sRNAs with an antisense function. In this study, the genome ofBorrelia burgdorferiwas subjected to different searches for sRNAs, including direct homology and comparative genomics searches and ortholog- and annotation-based search strategies. Two new sRNAs were found, one of which showed complementarity to therpoSregion, which it possibly controls by an antisense mechanism. The role of the other sRNA is unknown, although observed complementarities against particular mRNA sequences suggest an antisense mechanism. We suggest that the low level of sRNAs observed inB. burgdorferiis at least partly due to the presumed lack of both functional Hfq protein and RNase E activity.
Regulation of σBby an Anti- and an Anti-Anti-Sigma Factor inStreptomyces coelicolorin Response to Osmotic Stress
Authors: Lee Eun-Jin , Cho You-Hee , Kim Hyo-Sub , Ahn Bo-Eun , Roe Jung-Hye 
Published: December 2004

ABSTRACTσB, a homolog of stress-responsive σBofBacillus subtilis, controls both osmoprotection and differentiation inStreptomyces coelicolorA3 (2). Its gene is preceded byrsbAandrsbBgenes encoding homologs of an anti-sigma factor, RsbW, and its antagonist, RsbV, ofB. subtilis, respectively. Purified RsbA bound to σBand prevented σB-directed transcription from thesigBp1 promoter in vitro. AnrsbA-null mutant exhibited contrasting behavior to thesigBmutant, with elevatedsigBp1 transcription, no actinorhodin production, and precocious aerial mycelial formation, reflecting enhanced activity of σBin vivo. Despite sequence similarity to RsbV, RsbB lacks the conserved phosphorylatable serine residue and its gene disruption produced no distinct phenotype. RsbV (SCO7325) from a putative six-gene operon (rsbV-rsbR-rsbS-rsbT-rsbU1-rsbU) was strongly induced by osmotic stress in a σB-dependent manner. It antagonized the inhibitory action of RsbA on σB-directed transcription and was phosphorylated by RsbA in vitro. These results support the hypothesis that the rapid induction of σBtarget genes by osmotic stress results from modulation of σBactivity by the kinase-anti-sigma factor RsbA and its phosphorylatable antagonist RsbV, which function by a partner-switching mechanism. Amplified induction could result from a rapid increase in the synthesis of both σBand its inhibitor antagonist.
Interaction between the TolC and AcrA Proteins of a Multidrug Efflux System of
Escherichia coli
Authors: Husain Fasahath , Humbard Matthew , Misra Rajeev 
Published: December 2004

ABSTRACT

This paper provides the biochemical evidence for physical interactions between the outer membrane component, TolC, and the membrane fusion protein component, AcrA, of the major antibiotic efflux pump of
Escherichia coli
. Cross-linking between TolC and AcrA was independent of the presence of any externally added substrate of the efflux pump or of the pump protein, AcrB. The biochemical demonstration of a TolC-AcrA interaction is consistent with genetic studies in which extragenic suppressors of a mutant TolC strain were found in the
acrA
gene.
Activation of thegabOperon in an RpoS-Dependent Manner by Mutations That Truncate the Inner Core of Lipopolysaccharide inEscherichia coli
Authors: Joloba Moses L. , Clemmer Katy M. , Sledjeski Darren D. , Rather Philip N. 
Published: December 2004

ABSTRACTThegaboperon (gabDTPC) inEscherichia colifunctions in the conversion of γ-aminobutyrate to succinate. One component ofgaboperon regulation involves the RpoS sigma factor, which mediates activation at high cell density. Transposon mutagenesis was used to identify new genes that regulategaboperon expression in rich media. A Tn5tmpinsertion in thehldD(formerlyrfaD) gene increasedgabT::lacZexpression 12-fold. ThehldDgene product, an ADP-l-glycerol-d-mannoheptose-6-epimerase, catalyzes the conversion of ADP-d-glycerol-d-mannoheptose to ADP-l-glycerol-d-mannoheptose, a precursor for the synthesis of inner-core lipopolysaccharide (LPS). Defined mutations inhldE, required for heptose synthesis, andwaaF, required for the addition of the second heptose to the inner core, also resulted in high-levelgabT::lacZexpression. ThehldD,hldE, andwaaFmutants exhibited a mucoid colony phenotype due to production of a colanic acid capsule. However, in thehldD::catbackground, the high-level expression ofgabT::lacZwas independent of the regulatory components for colanic acid synthesis (rcsA,rcsB, andrcsC) and also independent ofmanC(cpsB), a structural gene for colanic acid synthesis. Activation ofgabT::lacZin thehldD::catbackground was dependent on the RpoS sigma factor. ThehldD::catmutation resulted in a sixfold increase in the levels of a translational RpoS-LacZ fusion and had a marginal effect on a transcriptional fusion. This study reveals a stress-induced pathway, mediated by loss of the LPS inner core, that increases RpoS translation andgaboperon expression inE. coli.
Legal Doctrines in Conflict:
Authors: Wiederhold Lutz 
Published: December 2004

AbstractAccording to Western legal historians, the closing of the door of Ijtihād shortly after the formation of the law schools resulted in a long period of sterility in Islamic legal thought and rigid adherence to traditional rules in legal practice. But what did Muslim scholars have in mind when they used the term Ijtihād? Do the sources point to any change in Muslim jurists' understanding of the notion of Ijtihād? And if so, is this change entirely the result of theoretical debate? Drawing on a wide variety of legal sources, supplemented by historiographical and prosopographical sources from the Mamluk and Ottoman periods, I attempt to answer these questions by drawing attention to the relationship between the debate on Ijtihād and the social and political circumstances and legal practices of particular Muslim societies.
Taqlīd, Legal Scaffolding and the Scope of Legal Injunctions in Post-Formative Theory:
Authors: Jackson Sherman 
Published: December 2004

AbstractThe controversy surrounding ijtihād and Taqlīd is well-known in modern scholarship. In the present essay, I offer an alternative to the leading views on this crux by treating the issue of scope in the jurisprudential writings of Shihāb al-Dīn al-Qarāfī as a reflection of the manner and direction in which the Islamic legal tradition tended to develop subsequent to the so-called settling down of the four schools of law. At the center of this development stood the highly intricate and spirited institution of Taqlīd, and I posit a causal relationship between the emergence of this institution and Muslim jurists' increased interest in issues such as scope. I also treat the technical aspects of al-Qarāfī's theory and compare it with the theories of a number of his predecessors.
The Social Logic of Taqlīd and the Rise of the Mukhataṣar
Authors: Fadel Mohammad 
Published: December 2004

AbstractThe study of the relationship between ijtihād and Taqlīd has been dominated by an approach that privileges ijtihād over Taqlīd on the assumption that the former is an intellectually superior mode of legal reasoning. By analyzing the role of Taqlīd in regulating the actions of muftīs and judges as discussed by post-6th/12th century jurists of the Mālikī school, I conclude that Taqlīd resulted from the desire to have uniform rules rather than as a result of intellectual stagnation. While ijtihād was individualistic and solipsistic, Taqlīd was the result of group interpretation that provided an objective basis upon which legal decisions and legal rulings could be described as being either substantively correct or incorrect. Viewed in this light, Taqlīd was originally a desire to limit the discretionary power of legal officials, especially those at the bottom of the legal hierarchy. The desire to possess uniform rules found its logical outcome in the legal genre of the mukhtaṣar as it emerged in the 7th/13th century. The mukhtaṣar functioned as the authoritative collection of a legal school's doctrine, and, for that reason, I argue that Islamic law in the age of mukhtaṣars is best understood as a codified Common Law.
The Legitimacy and Nature of Mawlid al-Nabī: (Analysis of a Fatwã)
Authors: Schussman Aviva 
Published: December 2004

AbstractIn 1993 Majallat al-Azhar published a fatwā issued in a response to a question regarding the form and religious legitimacy of the celebration of the Prophet Muhammad's birthday. The question was posed against the background of tension between the need and desire of Muslims to celebrate the festival — which is observed yearly almost everywhere in the Muslim world despite the fact that it includes features that resemble the pagan cult of saints, and the hesitancy or negative attitude of Muslim jurists with regard to the festival. In his response, the muftī confers legitimacy upon the festival within constraints defined by the Prophet's sunna. The vagueness of his answer, its lack of legal specifics, and its reliance on sources that contain popular motifs combine to indicate that the fatwā reflects the concession of a scholar to popular religion. Although the fatwā was intended to educate the public to celebrate the festival on a higher religious level, the muftī's approach to the subject seems to be popular rather than scholarly.
Shaykh Aḥmad Shākir and the Adoption of a Scientifically-Based Lunar Calendar
Authors: Moosa Ebrahim 
Published: December 2004

AbstractThe computation of the Muslim lunar calendar has been a subject of controversy for centuries. In the twentieth century, the debate surfaced again in different parts of the Muslim world. In Egypt, the distinguished jurist Aḥmad Shākir added his voice to the debate by writing a short treatise or risāla in which he argued that a calendar based on crescent sighting should be abandoned in favour of one based on scientific and astronomical computation. After providing some background information on Shākir and the lunar debate in Egypt and elsewhere in the Muslim world, I present an annotated translation of Shākir's treatise.
The Beginnings of the ḥanafī School in Iṣfahān
Authors: Tsafir Nurit 
Published: December 2004

AbstractThis essay, based mainly on two early Iṣfahānī biographical dictionaries, describes the introduction of the ḥanafī school to Iṣfahān. I argue that although schools of ḥadīth had a long history in Iṣfahān, the ḥanafī law school was also represented there from an early date. The ḥanafī legal method was practiced in the town around the middle of the second/eighth century, and ḥadīth on the authority of Abū ḥanīfa, transmitted to Iṣfahānī scholars through Abū ḥanīfa's pupil Zufar b. al-Hudhayl, started to circulate there around the same time. By the beginning of the third/ninth century a significant ḥanafī community had developed in Iṣfahān, and although schools of ḥadīth continued to be influential there, the Iṣfahānī ḥanafī community survived into the fourth/tenth century and was strengthened by the Saljūqs in the fifth/eleventh century and thereafter.