bluuebunny/crossref_metadata_2025_split huggingface dataset:
Function and regulation of the cyanobacterial genes lexA, recA and ruvB: LexA is critical to the survival of cells facing inorganic carbon starvation
Authors: Domain Francis , Houot Laetitia , Chauvat Franck , Cassier‐Chauvat Corinne 
Published: December 2004

SummaryThe cyanobacterial genes lexA, recA and ruvB were analysed in Synechocystis PCC6803, which is shown here to be more radiation resistant than the other unicellular model strain Synechococcus PCC7942. We found that cyanobacteria do not have an Escherichia coli‐type SOS regulon. The Synechocystis lexA and recA promoters were found to be strong and UV insensitive, unlike the ruvB promoter, which is weak and UV‐C inducible. Yet, lexA and recA are regulated by UV‐C, but the control is negative and occurs at the post‐transcriptional level. Two novel conserved elements were characterized in the lexA promoter: (i) an unusually long crucial box 5′‐TAAAATTTTGTATCTTTT‐3′ (−64, −47); and (ii) a negatively acting motif 5′‐TAT GAT‐3′ (−42, −37). These elements were not found in the recA promoter, which appeared to be unusually simple in harbouring only a single crucial element (i.e. the canonical −10 box). RuvB, operating in recombination‐dependent cellular processes, was found to be dispensable to cell growth, whereas LexA and RecA appeared to be critical to cell viability. Using DNA microarrays, we have identified 57 genes with expression that is altered, at least twofold, in response to LexA depletion. None of these genes is predicted to operate in DNA metabolism, arguing against the involvement of LexA in the regulation of DNA repair. Instead, most of the LexA‐responsive genes were known to be involved in carbon assimilation or controlled by carbon availability. Consistently, the growth of the LexA‐depleted strain was found to be strongly dependent on the availability of inorganic carbon.
Chimeras of P1‐type ATPases and their transcriptional regulators: contributions of a cytosolic amino‐terminal domain to metal specificity
Authors: Borrelly Gilles P. M. , Rondet Sabine A. M. , Tottey Stephen , Robinson Nigel J. 
Published: December 2004

SummaryZn2+‐responsive repressor ZiaR and Co2+‐responsive activator CoaR modulate production of P1‐type Zn2+‐ (ZiaA) and Co2+‐ (CoaT) ATPases respectively. What dictates metal selectivity? We show that Δ ziaΔcoa double mutants had similar Zn2+ resistance to Δzia single mutants and similar Co2+ resistance to Δcoa single mutants. Controlling either ziaA or coaT with opposing regulators restored no resistance to metals sensed by the regulators, but coincident replacement of the deduced cytosolic amino‐terminal domain CoaTN with ZiaAN (in ziaR‐p ziaA‐ziaANcoaT) conferred Zn2+ resistance to ΔziaΔcoa, Zn2+ content was lowered and residual Co2+ resistance lost. Metal‐dependent molar absorptivity under anaerobic conditions revealed that purified ZiaAN binds Co2+ in a pseudotetrahedral two‐thiol site, and Co2+ was displaced by Zn2+. Thus, the amino‐terminal domain of ZiaA inverts the metals exported by zinc‐regulated CoaT from Co2+ to Zn2+, and this correlates simplistically with metal‐binding preferences; KZiaAN Zn2+ tighter than Co2+. However, Zn2+ did not bleach Cu+‐ZiaAN, and only Cu+ co‐migrated with ZiaAN after competitive binding versus Zn2+. Bacterial two‐hybrid assays that detected interaction between the Cu+‐metallochaperone Atx1 and the amino‐terminal domain of Cu+‐transporter PacSN detected no interaction with the analogous, deduced, ferredoxin‐fold subdomain of ZiaAN. Provided that there is no freely exchangeable cytosolic Cu+, restricted contact with the Cu+‐metallochaperone can impose a barrier impairing the formation of otherwise favoured Cu+–ZiaAN complexes.
PhoP‐regulated Salmonella resistance to the antimicrobial peptides magainin 2 and polymyxin B
Authors: Shi Yixin , Cromie Michael J. , Hsu Fong‐Fu , Turk John , Groisman Eduardo A. 
Published: December 2004

SummaryIn Salmonella enterica, the PhoP–PhoQ two‐component system governs resistance to structurally different antimicrobial peptides including the alpha‐helical magainin 2, the β‐sheet defensins and the cyclic lipopeptide polymyxin B. To identify the PhoP‐regulated determinants mediating peptide resistance, we prepared a plasmid library from a phoP mutant, introduced it into a phoP mutant and selected for magainin‐resistant clones. One of the clones harboured the PhoP‐activated ugtL gene, deletion of which rendered Salmonella susceptible to magainin 2 and polymyxin B, but not defensin HNP‐1. We established that ugtL encodes an inner membrane protein that promotes the formation of monophosphorylated lipid A in the lipopolysaccharide. Inactivation of both ugtL and the regulatory gene pmrA, which controls lipid A modifications required for resistance to polymxyin B (but not to magainin 2) and is post‐transcriptionally activated by the PhoP–PhoQ system, resulted in a strain that was as susceptible to polymyxin B as a phoP mutant. The most frequently recovered clone harboured the yqjA gene, which we show is PhoP regulated and required for resistance to magainin 2 but not to polymyxin B or defensin HNP‐1. Our results indicate that different PhoP‐mediated modifications in lipid A are necessary for resistance to different antimicrobial peptides.
Targeted disruption of Plasmodium falciparum cysteine protease, falcipain 1, reduces oocyst production, not erythrocytic stage growth
Authors: Eksi Saliha , Czesny Beata , Greenbaum Doron C. , Bogyo Matthew , Williamson Kim C. 
Published: December 2004

SummaryCysteine proteases are currently targets for drug development in a number of parasitic diseases, including malaria. In Plasmodium falciparum, the parasite responsible for the most virulent form of human malaria, there are four members of the cathepsin L‐like family of cysteine proteases. Three of these (falcipains 2A, 2B and 3) are thought to be primarily involved in haemoglobin digestion, whereas falcipain 1 has recently been linked to erythrocyte invasion. Neither their expression nor their role in P. falciparum gametocytogenesis, which is required for malaria transmission, has been evaluated. In this study, RNA transcripts for the falcipain family members were identified as the parasite developed through all five stages of gametocytogenesis. Falcipain 1 transcript was upregulated in gametocytes, while levels of falcipain 2A/2B decreased in late‐stage gametocytes and gametes. To evaluate the function of falcipain 1, the gene was disrupted, and clones from independent transformations were isolated. The asexual growth of the falcipain 1 minus clones was not overtly affected, and they produced morphologically normal gametocytes and gametes. However, when falcipain 1 minus parasites were fed to a mosquito, oocyst production was reduced by 70–90%, suggesting an important role for falcipain 1 during parasite development in the mosquito midgut.
The human malaria parasite Plasmodium falciparum has distinct organelle‐specific lipoylation pathways
Authors: Wrenger Carsten , Müller Sylke 
Published: December 2004

SummaryLipoic acid is an essential cofactor of α‐keto acid dehydrogenase complexes (KADHCs). This study shows that Plasmodium falciparum possesses two distinct lipoylation pathways that are found in separate subcellular localizations. Lipoic acid synthesis comprising lipoic acid synthase and lipoyl‐ACP:protein N‐lipoyl transferase is present in the parasite's apicoplast, whereas the second pathway consisting of lipoic acid protein ligase is located in the parasite's mitochondrion. The two localizations were established by overexpressing green fluorescent protein fusions of the N‐terminal sequences of lipoic acid synthase and lipoic acid protein ligase in intraerythrocytic stages of P. falciparum. Northern and Western blot analyses revealed that the genes/proteins encoding lipoic acid synthase, lipoyl‐ACP:protein N‐lipoyl transferase and lipoic acid protein ligase are expressed maximally in the early and late stages of P. falciparum erythrocytic development. The functionality of the three proteins was proven by complementation of bacteria deficient in lipA and lipB. Our results show that P. falciparum possesses two independent pathways, with different locations, responsible for the post‐translational modification of KADHCs. Both pathways fundamentally differ from those in the human host. As KADHCs provide metabolites that are required for essential biosynthetic processes such as fatty acid biosynthesis and haem biosynthesis, the two lipoylation pathways of P. falciparum might be attractive therapeutic targets against malaria.
The impact of prophages on bacterial chromosomes
Authors: Canchaya Carlos , Fournous Ghislain , Brüssow Harald 
Published: December 2004

SummaryProphages were automatically localized in se‐quenced bacterial genomes by a simple semantic script leading to the identification of 190 prophages in 115 investigated genomes. The distribution of prophages with respect to presence or absence in a given bacterial species, the location and orientation of the prophages on the replichore was not homogeneous. In bacterial pathogens, prophages are particularly prominent. They frequently encoded virulence genes and were major contributors to the genetic individuality of the strains. However, some commensal and free‐living bacteria also showed prominent prophage contributions to the bacterial genomes. Lysogens containing multiple sequence‐related prophages can experience rearrangements of the bacterial genome across prophages, leading to prophages with new gene constellations. Transfer RNA genes are the preferred chromosomal integration sites, and a number of prophages also carry tRNA genes. Prophage integration into protein coding sequences can lead to either gene disruption or new proteins. The phage repressor, immunity and lysogenic conversion genes are frequently transcribed from the prophage. The expression of the latter is sometimes integrated into control circuits linking prophages, the lysogenic bacterium and its animal host. Prophages are apparently as easily acquired as they are lost from the bacterial chromosome. Fixation of prophage genes seems to be restricted to those with functions that have been co‐opted by the bacterial host.
Vibrio cholerae AphA uses a novel mechanism for virulence gene activation that involves interaction with the LysR‐type regulator AphB at the tcpPH promoter
Authors: Kovacikova Gabriela , Lin Wei , Skorupski Karen 
Published: December 2004

SummaryAphA is required for expression of the Vibrio cholerae virulence cascade and for its regulation by quorum sensing. In order to activate transcription, AphA functions together with a second protein, the LysR‐type regulator AphB, at the tcpPH promoter. As AphA is a member of a new and largely uncharacterized regulator family, random mutagenesis was used to gain insights into how this protein activates transcription. As shown here, 17 amino acid substitutions were identified in AphA that reduced expression of the tcpPH promoter and prevented the protein from binding DNA. The amino acids involved in DNA recognition inferred from a dominant‐negative analysis were located throughout the N‐terminal domain from amino acids 18 to 67. This region of AphA has a conserved domain architecture similar to that of MarR, a multiple antibiotic resistance repressor. The analogous positions of the dominant‐negative mutations in AphA and MarR confirm that the DNA‐binding domains of these proteins are similar and indicate that AphA is a new member of the winged helix family of transcription factors. We also show that AphB is capable of rescuing two of the DNA binding‐defective AphA mutants, suggesting that the proteins interact directly on the DNA. Disruption of this interaction by insertion of half a helical turn between the two binding sites prevented AphB from rescuing the mutants and prevented the expression of the virulence cascade in a wild‐type background. These results provide a novel mechanism for the initiation of virulence gene expression at tcpPH.
Identification of mutator genes and mutational pathways in Escherichia coli using a multicopy cloning approach
Authors: Yang Hanjing , Wolff Erika , Kim Mandy , Diep Amy , Miller Jeffrey H. 
Published: December 2004

SummaryWe searched for genes that create mutator phenotypes when put on to a multicopy plasmid in Escherichia coli. In many cases, this will result in overexpression of the gene in question. We constructed a random shotgun library with E. coli genomic fragments between 3 and 5 kbp in length on a multicopy plasmid vector that was transformed into E. coli to screen for frameshift mutators. We identified a total of 115 independent genomic fragments that covered 17 regions on the E. coli chromosome. Further studies identified 12 genes not previously known as causing mutator phenotypes when overproduced. A striking finding is that overproduction of the multidrug resistance transcription regulator, EmrR, results in a large increase in frameshift and base substitution mutagenesis. This suggests a link between multidrug resistance and mutagenesis. Other identified genes include those encoding DNA helicases (UvrD, RecG, RecQ), truncated forms of the DNA mismatch repair protein (MutS) and a primosomal component (DnaT), a negative modulator of initiation of replication/GATC‐binding protein (SeqA), a stationary phase regulator AppY, a transcriptional regulator PaaX and three putative open reading frames, ycgW, yfjY and yjiD, encoding hypothetical proteins. In addition, we found three genes encoding proteins that were previously known to cause mutator effects under overexpression conditions: error‐prone polymerase IV (DinB), DNA methylase (Dam) and sigma S factor (RpoS). This genomic strategy offers an approach to identify novel mutator effects resulting from the multicopy cloning (MCC) of specific genes and therefore complementing the conventional gene inactivation approach to finding mutators.
A proteomic determination of cold adaptation in the Antarctic archaeon, Methanococcoides burtonii
Authors: Goodchild Amber , Saunders Neil F. W. , Ertan Haluk , Raftery Mark , Guilhaus Michael , Curmi Paul M. G. , Cavicchioli Ricardo 
Published: December 2004

SummaryA global view of the biology of the cold‐adapted archaeon Methanococcoides burtonii was achieved using proteomics. Proteins specific to growth at 4°C versus Topt (23°C) were identified by mass spectrometry using the draft genome sequence of M. burtonii. mRNA levels were determined for all genes identified by proteomics, and specific enzyme assays confirmed the protein expression results. Key aspects of cold adaptation related to transcription, protein folding and metabolism, including specific roles for RNA polymerase subunit E, a response regulator and peptidyl prolyl cis/trans isomerase. Heat shock protein DnaK was expressed during growth at Topt, indicating that growth at ‘optimal’ temperatures was stressful for this cold‐adapted organism. Expression of trimethylamine methyltransferase involves contiguous translation of two open reading frames, which is likely to result from incorporation of pyrrolysine at an amber stop codon. Thermal regulation in M. burtonii is achieved through complex gene expression events involving gene clusters and operons, through to protein modifications.
Activation of pleiotropic drug resistance by the J‐protein and Hsp70‐related proteins, Zuo1 and Ssz1
Authors: Eisenman Helene C. , Craig Elizabeth A. 
Published: December 2004

SummarySsz1 (Pdr13) and Zuo1, members of the Hsp70 and J‐protein molecular chaperone families, respectively, form a heterodimer and function on the ribosome with the Hsp70, Ssb, presumably assisting folding of newly synthesized polypeptides. As it has also been reported that Ssz1 induces pleiotropic drug resistance (PDR) when overexpressed, a possible role for Zuo1 in PDR was investigated. The C‐terminal domain of Zuo1, which is dispensable for Zuo1's chaperone function on the ribosome, is both necessary and sufficient for PDR induction by Zuo1. A single domain of Ssz1, the N‐terminal ATPase domain, is sufficient for PDR induction as well, indicating that Ssz1 does not function as a chaperone in PDR. No role for Ssb was found in PDR; overexpression did not affect PDR, nor was its presence required for Ssz1's or Zuo1's effect on PDR. As our results also indicate that Ssz1 and Zuo1 must be free of ribosomes to induce PDR, we propose that Ssz1's and Zuo1's function in PDR is distinct from their role as ribosome‐associated co‐chaperones and may be regulatory in nature.
Hfq is essential for Vibrio cholerae virulence and downregulates σE expression
Authors: Ding Yanpeng , Davis Brigid M. , Waldor Matthew K. 
Published: December 2004

SummaryHfq is an RNA‐binding protein that interacts with both small untranslated RNAs (sRNAs) and mRNAs to modulate gene expression post‐transcriptionally. In Escherichia coli and Salmonella typhimurium, Hfq is required for efficient expression of the stationary phase sigma factor σS, and consequently is critical for Salmonella virulence. We have found that Hfq is also essential for the virulence of Vibrio cholerae, as strains lacking hfq fail to colonize the suckling mouse intestine. Deletion of the V. cholerae hfq does not prevent production of σS, nor does it prevent expression of TCP, V. cholerae's primary colonization factor. The expression and activity of the alternative sigma factor σE are dramatically increased in a V. cholerae hfq mutant. Comparison of the transcriptome of an hfq mutant with that of an rseA mutant, which also overexpresses σE, revealed that σE controls approximately half the genes found to be upregulated in the hfq mutant. However, increased σE does not appear to account for this strain's reduced virulence. It is likely that sRNAs, in conjunction with Hfq, are critical regulators of V. cholerae pathogenicity.
Euroconference on the Biology of Type IV Secretion Processes: bacterial gates into the outer world
Authors: Llosa Matxalen , O'Callaghan David 
Published: December 2004

SummaryType IV secretion systems (T4SSs) mediate both protein and ssDNA secretion from a wide range of bacteria into virtually any cell type or into the milieu. It is this versatility that confers on them the ability to participate in many processes of bacterial life that imply communication with their environment. Type IV secretion systems are involved in horizontal DNA transfer to other bacteria and to plant cells, in DNA uptake from the milieu, in toxin secretion into the milieu, and in the injection of virulence factors into the eukaryotic host cell in a number of mammalian and plant pathogens. Recently, a EuroConference addressed the different aspects of the biology of these transmembrane multiprotein complexes, from the crystal structure of the individual components to the modification that the secreted substrates induce in the recipient cell. Significant progress has been made in the understanding of the molecular architecture and mechanism of secretion. The analysis of protein–protein interactions confirms the role of coupling proteins as substrate recruiters for the transporter. The VirB10 component of the complex has come up as a strong candidate for signal transducer. The wide range of effects on the recipient suggests that many effector proteins are secreted. New effector proteins are being identified for both plant and animal pathogens, as are their targets within the host cells. New T4SS members are being identified that perform novel roles, beyond DNA transfer and virulence, such as establishment of symbiotic processes. Our current knowledge of the Biology of Type IV Secretion Processes increases our ability to exploit them as biotechnological tools or to use them as new targets for inhibitors that could constitute a new generation of antimicrobials in the near future.
Modelling the establishment and spread of autotetraploid plants in a spatially heterogeneous environment
Authors: Li B.-H. , Xu X.-M. , Ridout M. S. 
Published: December 2004

Abstract
The establishment and spread of autotetraploids from an original diploid population in a heterogeneous environment were studied using a stochastic simulation model. Specifically, we investigated the effects of heterogeneous habitats and nonrandom pollen/seed dispersal on the critical value (μ) of unreduced 2n gamete production necessary for the establishment of autotetraploids as predicted by deterministic models. Introduction of a heterogeneous environment with random pollen/seed dispersal had little effect on the μ value. In contrast, incorporating nonrandom pollen/seed dispersal into a homogeneous environment considerably reduced the μ value. Incorporating both heterogeneous habitats and nonrandom pollen/seed dispersal may lead either to an increase or to a decrease in the μ value compared to that with random dispersal, indicating that the two factors interact in a complex way.
Trade-offs between sexual and clonal reproduction in an aquatic plant: experimental manipulations vs. phenotypic correlations
Authors: Thompson F. L. , Eckert C. G. 
Published: December 2004

Abstract
That trade-offs result from the allocation of limited resources is a central concept of life history evolution. We quantified trade-offs between sexual and clonal reproduction in the aquatic plant, Butomus umbellatus, by experimentally manipulating sexual investment in two distinct nutrient environments. Increasing seed production caused a significant but nonlinear trade-off. Pollinating half of all flowers strongly reduced clonal bulbil production, but pollinating the remaining flowers did not cause any further trade-off. Trade-offs were not stronger under low nutrient conditions that clearly limited plant growth. Experimentally induced trade-offs were not reflected in negative phenotypic correlations between sexual and clonal allocation among plants within eight populations grown in a uniform greenhouse environment. Diminishing effects of increased sexual allocation plus a lack of accord between experimental manipulations and phenotypic correlations suggest that trade-offs between sexual and clonal reproduction are unlikely to constrain the evolution of reproductive strategy in this species.
Variable selection in Platanthera bifolia (Orchidaceae): phenotypic selection differed between sex functions in a drought year
Authors: Maad J. , Alexandersson R. 
Published: December 2004

Abstract
We estimated selection on three morphological characters in the hermaphroditic, hawkmoth-pollinated orchid Platanthera bifolia and explored selection surfaces through male and female function. The work was carried out in northern Sweden during two flowering seasons (1994 and 1995) in one natural population and one season (1995) in another natural population. Fitness was estimated as number of pollinia removed (male function) and number of fruits produced (female function). We detected directional selection towards larger inflorescence size (flower number) through both sex functions in both populations in 1995. In 1994, with an unusually dry growing season, 78% of the individuals failed to set any fruit, and there was selection for larger inflorescences only through male function. In this year, there was selection towards longer flower spurs, which could be a direct or indirect effect of spurs being shortened by drought. The results demonstrate that selection patterns may vary temporally and spatially, and that the ‘male function hypothesis’ may be applicable as female function is more resource dependent than male function.