bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unique mechanistic features of post‐translational regulation of glutamine synthetase activity in Methanosarcina mazei strain Gö1 in response to nitrogen availability
Authors: Ehlers Claudia , Weidenbach Katrin , Veit Katharina , Forchhammer Karl , Schmitz Ruth A. 
Published: March 2005

SummaryPII‐like signal transduction proteins are found in all three domains of life and have been shown to play key roles in the control of bacterial nitrogen assimilation. This communication reports the first target protein of an archaeal PII‐like protein, representing a novel PII receptor. The GlnK1 protein of the methanogenic archaeon Methanosarcina mazei strain Gö1 interacts and forms stable complexes with glutamine synthetase (GlnA1). Complex formation with GlnK1 in the absence of metabolites inhibits the activity of GlnA1. On the other hand, the activity of this enzyme is directly stimulated by the effector molecule 2‐oxoglutarate. Moreover, 2‐oxoglutarate antagonized the inhibitory effects of GlnK1 on GlnA1 activity but did not prevent GlnK1/GlnA1 complex formation. On the basis of these findings, we hypothesize that besides the dominant effector molecule 2‐oxoglutarate, the nitrogen sensor GlnK1 allows finetuning control of the glutamine synthetase activity under changing nitrogen availabilities and propose the following model. (i) Under nitrogen limitation, increasing concentrations of 2‐oxoglutarate stimulate maximal GlnA1 activity and transform GlnA1 into an activated conformation, which prevents inhibition by GlnK1. (ii) Upon a shift to nitrogen sufficiency after a period of nitrogen limitation, GlnA1 activity is reduced by decreasing internal 2‐oxoglutarate concentrations through diminished direct activation and by GlnK1 inhibition.
A pathway‐specific transcriptional regulatory gene for nikkomycin biosynthesis in Streptomyces ansochromogenes that also influences colony development
Authors: Liu Gang , Tian Yuqing , Yang Haihua , Tan Huarong 
Published: March 2005

SummaryDNA sequence analysis of a 7.5 kb XhoI DNA fragment from the region flanking the nikkomycin biosynthesis gene cluster in Streptomyces ansochromogenes revealed one 3.3 kb open reading frame (ORF), designated sanG. The deduced product of sanG (1061 amino acids), which is similar to PimR of Streptomyces natalensis, contains an OmpR‐like DNA binding domain in its N‐terminal portion and A‐ and B‐type nucleotide binding motifs in the middle of the protein. Disruption of sanG abolished nikkomycin biosynthesis, reduced sporulation and led to brown pigment accumulation. All aspects of this complex phenotype were complemented by a single copy sanG which was integrated into the chromosome. The introduction of multiple copies of sanG resulted in increased nikkomycin production. S1 mapping results indicated that sanG is transcribed from at least three promoters (P1, P2 and P3), P1 being strongly upregulated when production of nikkomycins starts. Two putative transcription units for nikkomycin biosynthesis, starting from sanN and sanO, are dependent on the expression of sanG, whereas a putative transcription unit starting from sanF was not regulated by sanG. These results suggested that sanG encodes a transcriptional activator important for nikkomycin biosynthesis that, unusually, also has pleiotropic effects on secondary metabolism and development.
A new in vivo termination function for DNA polymerase I of Escherichia coli K12
Authors: Markovitz Alvin 
Published: March 2005

SummaryEscherichia coli deleted for the tus gene are viable. Thus there must be at least one other mechanism for terminating chromosome synthesis. The tus deletion strain yielded a small fraction of cells that overproduce DNA, as determined by flow cytometry after run‐out chromosome replication in the presence of rifampicin and cephalexin. A plasmid, paraBAD tus+, prevented the excess DNA replication only when arabinose was added to the medium to induce the synthesis of the Tus protein. Transduction studies were done to test whether or not additional chromosomal deletions could enhance the excess chromosome replication in the tus deletion strain. A strain containing a second deletion in metE udp overproduced DNA at a high level during run‐out replication. Further studies demonstrated that a spontaneous unknown mutation had occurred during the transduction. This mutation was mapped and sequenced. It is polA(G544D). Transduction of polA(G544D) alone into the tus deletion strain produced the high DNA overproduction phenotype. The polA(G544D) and six other polA alleles were then tested in wild‐type and in tus deletion backgrounds. The two alleles with low levels of 5′→3′ exonuclease (exo) overproduced DNA while those with either high or normal exo overproduce much less DNA in run‐out assays in the wild‐type background. In contrast, all seven mutant polA alleles caused the high DNA overproduction phenotype in a tus deletion background. To explain these results we propose a new in vivo function for wild‐type DNA polymerase I in chromosome termination at site(s) not yet identified.
Genetic analysis of mch mutants in two Methanosarcina species demonstrates multiple roles for the methanopterin‐dependent C‐1 oxidation/reduction pathway and differences in H2 metabolism between closely related species
Authors: Guss Adam M. , Mukhopadhyay Biswarup , Zhang Jun Kai , Metcalf William W. 
Published: March 2005

SummaryA mutation in the mch gene, encoding the enzyme 5,10‐methenyl tetrahydromethanopterin (H4MPT) cyclohydrolase, was constructed in vitro and recombined onto the chromosome of the methanogenic archaeon Methanosarcina barkeri. The resulting mutant does not grow in media using H2/CO2, methanol, or acetate as carbon and energy sources, but does grow in media with methanol/H2/CO2, demonstrating its ability to utilize H2 as a source of electrons for reduction of methyl groups. Cell suspension experiments showed that methanogenesis from methanol or from H2/CO2 is blocked in the mutant, explaining the lack of growth on these substrates. The corresponding mutation in Methanosarcina acetivorans C2A, which cannot grow on H2/CO2, could not be made in wild‐type strains, but could be made in strains carrying a second copy of mch, suggesting that M. acetivorans is incapable of methyl group reduction using H2. M. acetivorans mch mutants could also be constructed in strains carrying the M. barkeri ech hydrogenase operon, suggesting that the block in the methyl reduction pathway is at the level of H2 oxidation. Interestingly, the ech‐dependent methyl reduction pathway of M. acetivorans involves an electron transport chain distinct from that used by M. barkeri, because M. barkeri ech mutants remain capable of H2‐dependent methyl reduction.
Induction of Staphylococcus epidermidis biofilm formation via proteolytic processing of the accumulation‐associated protein by staphylococcal and host proteases
Authors: Rohde Holger , Burdelski Christoph , Bartscht Katrin , Hussain Muzaffar , Buck Friedrich , Horstkotte Matthias A. , Knobloch Johannes K.‐M. , Heilmann Christine , Herrmann Mathias , Mack Dietrich 
Published: March 2005

SummaryBecause of its biofilm forming potential Staphylococcus epidermidis has evolved as a leading cause of device‐related infections. The polysaccharide intercellular adhesin (PIA) is significantly involved in biofilm accumulation. However, infections because of PIA‐negative strains are not uncommon, suggesting the existence of PIA‐independent biofilm accumulation mechanisms. Here we found that biofilm formation in the clinically significant S. epidermidis 5179 depended on the expression of a truncated 140 kDa isoform of the 220 kDa accumulation‐associated protein Aap. As expression of the truncated Aap isoform leads to biofilm formation in aap‐negative S. epidermidis 1585, this domain mediates intercellular adhesion in a polysaccharide‐independent manner. In contrast, expression of full‐length Aap did not lead to a biofilm‐positive phenotype. Obviously, to gain adhesive function, full‐length Aap has to be proteolytically processed through staphylococcal proteases as demonstrated by inhibition of biofilm formation by α2‐macroglobulin. Importantly, also exogenously added granulocyte proteases activated Aap, thereby inducing biofilm formation in S. epidermidis 5179 and four additional, independent clinical S. epidermidis strains. It is therefore reasonable to assume that in vivo effector mechanisms of the innate immunity can directly induce protein‐dependent S. epidermidis cell aggregation and biofilm formation, thereby enabling the pathogen to evade clearance by phagocytes.
MpcT is the transducer for membrane potential changes in Halobacterium salinarum
Authors: Koch Matthias K. , Oesterhelt Dieter 
Published: March 2005

SummaryIn Halobacterium salinarum mutants containing either of the light‐driven ion pumps bacteriorhodopsin (H+) or halorhodopsin (Cl–) as their only retinal protein, a decrease of irradiance in the absence of respiration causes a phototactic response. The conversion of the causal event, a decrease of proton motive force across the cell membrane, into a reversal of flagellar motor rotational direction was expected to involve a transducer. Via deletion analysis of all 18 known and putative halobacterial transducer (htr) genes, we found that Htr14, a methylatable membrane‐bound transducer lacking an extracellular domain, mediates the biological response, which includes adaptive methylation. Based on a minimal stimulus length of 200 ms and the determined cytoplasmic buffering capacity, we conclude that the change in the membrane potential (ΔΨ), and not that of the internal pH, is the signal‐generating event. Htr14 was therefore renamed to Membrane potential change Transducer, or MpcT. It is the first transducer for which the causative stimulus could be narrowed to a change in ΔΨ, as opposed to a change in pH or cellular redox state.
Integration and excision by the large serine recombinase φRv1 integrase
Authors: Bibb Lori A. , Hancox Maria I. , Hatfull Graham F. 
Published: March 2005

SummaryThe Mycobacterium tuberculosis prophage‐like element φRv1 encodes a site‐specific recombination system utilizing an integrase of the serine recombinase family. Recombination occurs between a putative attP site and the host chromosome, but is unusual in that the attB site lies within a redundant repetitive element (REP13E12)  of  which  there  are  seven  copies  in  the M. tuberculosis genome; four of these elements contain attB sites suitable for φRv1 integration in vivo. Although the mechanism of directional control of large serine integrases is poorly understood, a recombination directionality factor (RDF) has been identified that is required for φRv1 integrase‐mediated excisive recombination in vivo. Here we describe defined in vitro recombination reactions for both φRv1 integrase‐mediated integration and excision and show that the φRv1 RDF is not only required for excision but inhibits integrative recombination; neither reaction requires DNA supercoiling, host factors, or high‐energy cofactors. Integration, excision and excise‐mediated inhibition of integration require simple substrates sites, indicating that the control of directionality does not involve the manipulation of higher‐order protein–DNA architectures as described for the tyrosine integrases.
Functional analysis of the Campylobacter jejuni N‐linked protein glycosylation pathway
Authors: Linton Dennis , Dorrell Nick , Hitchen Paul G. , Amber Saba , Karlyshev Andrey V. , Morris Howard R. , Dell Anne , Valvano Miguel A. , Aebi Markus , Wren Brendan W. 
Published: March 2005

SummaryWe describe in this report the characterization of the recently discovered N‐linked glycosylation locus of the human bacterial pathogen Campylobacter jejuni, the first such system found in a species from the domain Bacteria. We exploited the ability of this locus to function in Escherichia coli to demonstrate through mutational and structural analyses that variant glycan structures can be transferred onto protein indicating the relaxed specificity of the putative oligosaccharyltransferase PglB. Structural data derived from these variant glycans allowed us to infer the role of five individual glycosyltransferases in the biosynthesis of the N‐linked heptasaccharide. Furthermore, we show that C. jejuni‐ and E. coli‐derived pathways can interact in the biosynthesis of N‐linked glycoproteins. In particular, the E. coli encoded WecA protein, a UDP‐GlcNAc: undecaprenylphosphate GlcNAc‐1‐phosphate transferase involved in glycolipid biosynthesis, provides for an alternative N‐linked heptasaccharide biosynthetic pathway bypassing the requirement for the C. jejuni‐derived glycosyltransferase PglC. This is the first experimental evidence that biosynthesis of the N‐linked glycan occurs on a lipid‐linked precursor prior to transfer onto protein. These findings provide a framework for understanding the process of N‐linked protein glycosylation in Bacteria and for devising strategies to exploit this system for glycoengineering.
Neisseria gonorrhoeae secretes chromosomal DNA via a novel type IV secretion system
Authors: Hamilton Holly L. , Domínguez Nadia M. , Schwartz Kevin J. , Hackett Kathleen T. , Dillard Joseph P. 
Published: March 2005

SummaryThe process of DNA donation for natural transformation of bacteria is poorly understood and has been assumed to involve bacterial cell death. Recently in Neisseria gonorrhoeae we found that mutations in three genes in the gonococcal genetic island (GGI) reduced the ability of a strain to act as a donor in transformation and to release DNA into the culture. To better characterize the GGI and the process of DNA donation, the 57 kb genetic island was cloned, sequenced and subjected to insertional mutagenesis. DNA sequencing revealed that the GGI has characteristics of a horizontally acquired genomic island and encodes homologues of type IV secretion system proteins. The GGI was found to be incorporated near the chromosomal replication terminus at the dif site, a sequence targeted by the site‐specific recombinase XerCD. Using a plasmid carrying a small region of the GGI and the associated dif site, we demonstrated that this model island could be integrated at the dif site in strains not carrying the GGI and was spontaneously excised from that site. Also, we were able to delete the entire 57 kb region by transformation with DNA from a strain lacking the GGI. Thus the GGI was likely acquired and integrated into the gonococcal chromosome by site‐specific recombination and may be lost by site‐specific recombination or natural transformation. We made mutations in six putative type IV secretion system genes and assayed these strains for the ability to secrete DNA. Five of the mutations greatly reduced or completely eliminated DNA secretion. Our data indicate that N. gonorrhoeae secretes DNA via a specific process. Donated DNA may be used in natural transformation, contributing to antigenic variation and the spread of antibiotic resistance, and it may modulate the host immune response.
Tethering the Z ring to the membrane through a conserved membrane targeting sequence in FtsA
Authors: Pichoff Sebastien , Lutkenhaus Joe 
Published: March 2005

SummaryThe cytokinetic Z ring is required for bacterial cell division. It consists of polymers of FtsZ, the bacterial ancestor of eukaryotic tubulin, linked to the cytoplasmic membrane. Formation of a Z ring in Escherichia coli occurs as long as one of two proteins, ZipA or FtsA, is present. Both of these proteins bind FtsZ suggesting that they might function to tether FtsZ filaments to the membrane. Although ZipA has a transmembrane domain and therefore can function as a membrane anchor, interaction of FtsA with the membrane has not been explored. In this study we demonstrate that FtsA, which is structurally related to eukaryotic actin, has a conserved C‐terminal amphipathic helix that is essential for FtsA function. It is required to target FtsA to the membrane and subsequently to the Z ring. As FtsA is much more widely conserved in bacteria than ZipA, it is likely that FtsA serves as the principal membrane anchor for the Z ring.
Targeted deletion of Plasmodium knowlesi Duffy binding protein confirms its role in junction formation during invasion
Authors: Singh Agam P. , Ozwara Hastings , Kocken Clemens H. M. , Puri Sunil K. , Thomas Alan W. , Chitnis Chetan E. 
Published: March 2005

SummaryRed cell invasion by Plasmodium merozoites involves multiple steps such as attachment, apical reorientation, junction formation and entry into a parasitophorous vacuole. These steps are mediated by specific molecular interactions. P. vivax and the simian parasite P. knowlesi require interaction with the Duffy blood group antigen to invade human erythrocytes. P. vivax and P. knowlesi Duffy binding proteins (PvDBP and PkDBP), which bind the Duffy antigen during invasion, share regions of sequence homology and belong to a family of erythrocyte binding proteins (EBPs). By deletion of the gene that encodes PkDBP, we demonstrate that interaction of PkDBP with the Duffy antigen is absolutely necessary for invasion of human erythrocytes by P. knowlesi. Electron microscopy studies reveal that PkDBP knockout parasites are unable to form a junction with human erythrocytes. The interaction of PkDBP with the Duffy antigen is thus necessary for the critical step of junction formation during invasion. These studies provide support for development of intervention strategies that target EBPs to inhibit junction formation and block erythrocyte invasion by malaria parasites.
Qri2/Nse4, a component of the essential Smc5/6 DNA repair complex
Authors: Hu Bin , Liao Chunyan , Millson Stefan H. , Mollapour Mehdi , Prodromou Chrisostomos , Pearl Laurence H. , Piper Peter W. , Panaretou Barry 
Published: March 2005

SummaryWe demonstrate a role for Qri2 in the essential DNA repair function of the Smc5/6 complex inSaccharomyces cerevisiae. We generated temperature‐sensitive (ts) mutants inQRI2and characterized their properties. The mutants arrest after S phase and prior to mitosis. Furthermore, the arrest is dependant on the Rad24 checkpoint, and is also accompanied by phosphorylation of the Rad53 checkpoint effector kinase. The mutants also display genome instability and are sensitive to agents that damage DNA. Two‐hybrid screens reveal a physical interaction between Qri2 and proteins that arenon‐Smcelements of the Smc5/6 DNA repair complex, which is why we propose the nameNSE4for the open reading frame previously known asQRI2. A key role for Nse4 in Smc5/6 function is likely, as overexpressing known subunits of the Smc5/6 complex suppressesnse4tscell cycle arrest. Thense4tsgrowth arrest is non‐lethal and unlike the catastrophic nuclear fragmentation phenotype ofsmc6tsmutants, the nucleus remains intact; replicative intermediates and sheared DNA are not detected. This could imply a role for Nse4 in maintenance of higher order chromosome structure.
Lithospheric structure beneath the south‐eastern Zagros Mountains, Iran: recent slab break‐off?
Authors: Molinaro M. , Zeyen H. , Laurencin X. 
Published: March 2005

AbstractIntegrated lithospheric modelling, based on the combined interpretation of gravity, geoid and topography data sets, highlights a previously undocumented lithospheric thinning beneath the Zagros collisional belt (Iran), which we propose to relate to recent slab break‐off at the continent–ocean transitional lithosphere. Recent published data on the distribution of seismicity at depth support this interpretation. In agreement with other published models for the Zagros Mountains, the overlying crust exhibits, by contrast, a noticeable thickening, reaching a maximum of 52 km. The consequent thermal uplift expected from slab break‐off is suggested to have modified the Zagros wedge taper and triggered the recently documented switch from thin‐skinned to thick‐skinned deformation in the Zagros Fold–Thrust Belt.
A tephra‐based correlation between the Faroe Islands and the Norwegian Sea raises questions about chronological relationships during the last interglacial
Authors: Wastegård Stefan , Björck Svante , Greve Charlotte , Rasmussen Tine L. 
Published: March 2005

AbstractMarine ash zones from the last interglacial period have been described from cores from the North Atlantic and an ash zone from the middle part of the interglacial has been observed in connection with a major cooling event. Here we present evidence for a coeval ash zone in a terrestrial site on the Faroe Islands. The investigated sediments are correlated with the upper part of oxygen isotope stage 5e and the beginning of stage 5d. The Eemian climatic optimum is represented in the lower part of the sequence close to the first occurrence of the ash zone. A tephra‐based correlation suggests that the climatic optimum was synchronous with the marine record from the Norwegian Sea, but several thousand years later than in Eemian sections of west central Europe. However, many questions on the chronological relationship between the Eemian and oxygen isotope stage 5e still remain to be answered.
Long‐runout pyroclastic surge on a Cretaceous alluvial plain, Republic of Korea
Authors: Sohn Y. K. , Jeong J. O. , Son M. 
Published: March 2005

AbstractPyroclastic surge is a dilute and turbulent flow of volcanic gas and tephra that is commonly generated during explosive volcanic eruptions and can threaten lives along its flow paths. Assessing its travel distance and delineating future volcanic hazards have therefore been major concerns of volcanologists. Historical eruptions show that most pyroclastic surges travel a few tens of kilometres or less from their sources. Aeolian or aquagene processes have therefore been evoked for the emplacement of supposed surge deposits much beyond this distance. Here we show that a Cretaceous tuff bed in Korea was emplaced by an exceptionally powerful pyroclastic surge that flowed as far as the most powerful pyroclastic flows that formed the low‐aspect‐ratio ignimbrites (LARI). This has significant implications for interpreting ancient volcanic eruptions and delineating volcanic hazards by pyroclastic surges, and casts intriguing questions on the eruption dynamics and physics of long‐runout pyroclastic surges and their distinction from LARI‐forming pyroclastic flows.
Mountain building‐enhanced continental weathering and organic carbon burial as major causes for climatic cooling at the Frasnian–Famennian boundary (c. 376 Ma)?
Authors: Averbuch O. , Tribovillard N. , Devleeschouwer X. , Riquier L. , Mistiaen B. , Van Vliet‐Lanoe B. 
Published: March 2005

AbstractThe Late Devonian was a period of drastic environmental changes, as exemplified by a major biotic crisis at the Frasnian–Famennian boundary (FFB) and the onset in Famennian times of glaciations across southern Gondwana. Worldwide evidence for the coeval development of the major Acadian–Eovariscan belt led us to propose a model relating the Late Frasnian–Famennian environmental perturbations to extensive continental uplift through two atmospheric CO2‐depleting mechanisms: (1) the intensification of silicate weathering on the continental areas as attested by a major rise in the87Sr/86Sr composition of sea water at the FFB; and (2) the massive burial of organic carbon (Kellwasser events) in partially confined basins due to the collisional‐induced reduction of equatorial oceanic communications between the Palaeotethysian and Panthalassic oceans. This process is also suggested to have been controlled by an important primary productivity connected to an increased nutrient availability triggered by the enhanced continental run‐off.