bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence and molecular analysis of the nifL gene of Azotobacter vinelandii
Authors: Blanco Gonzalo , Drummond Martin , Woodley Paul , Kennedy Christina 
Published: October 2006

SummaryIn both Klebsiella pneumoniae and Azotobacter vinelandii the nifL gene, which encodes a negative regulator of nitrogen fixation, lies immediately upstream of nifA. We have sequenced the A. vinelandii nifL gene and found that it is more homologous in its C‐terminal domain to the histidine protein kinases (HPKs) than Is K. pneumoniae NifL. In particular A. vinelandii NifL contains a conserved histidine at a position shown to be phosphorylated in other systems. Both NifL proteins are homologous in their N‐termini to a part of the Halobacterium halobium bat gene product; Bat is involved in regulation of bacterio‐opsin, the expression of which is oxygen sensitive. The same region showed homology to the haembinding N‐terminai domain of the Rhizobium meliloti fixL gene product, an oxygen‐sensing protein. Like K. pneumoniae NifL, A. vinelandii NifL is shown here to prevent expression of nif genes in the presence of NH+4 or oxygen. The sequences found homologous in the C‐terminal regions of NifL, FixL and Bat might therefore be involved in oxygen binding or sensing. An in‐frame deletion mutation in the nifL coding region resulted in loss of repression by NH+4 and the mutant excreted high amounts of ammonia during nitrogen fixation, thus confirming a phenotype reported earlier for an insertion mutation. In addition, nifLA are cotranscribed in A. vinelandii as in K. pneumoniae, but expression from the A. vinelandii promoter requires neither RpoN nor NtrC.
Molecular characterization of a fungal secondary metabolism promoter: transcription of the Aspergillus nidulans isopenicillin N synthetase gene is modulated by upstream negative elements
Authors: Perez‐Esteban Beatriz , Orejas Margarita , Gómez‐Pardo Emilia , Peñalva Miguel Angel 
Published: October 2006

SummaryThe Aspergillus nidulans IPNS gene, encoding isopenicillin N synthetase, is a secondary metabolism gene. It is contiguous to, but divergently transcribed from, the ACVS gene at the penicillin gene cluster. The untranslated region between both ORFs is 872bp long. Here we present the physical and functional characterization of the IPNS transcriptional unit. Transcriptional start point (tsp) mapping reveals heterogeneity at the 5′‐end of the mRNA, with a major start at −106 relative to the initiation codon. This indicates that the actual length of the non‐transcribed intergenic region is 525bp. Functional elements in the IPNS upstream region have been defined by assaying β‐galactosidase activity in extracts from recombinant strains carrying deletion derivatives of the IPNS promoter fused to lacZ, integrated in single copy at the argB locus. Strains were grown in penicillin production broth under carbon catabolite repressing or derepressing conditions. The results of deletion analysis indicate that: (i) the IPNS promoter is mostly regulated by negative controls that act upon a high basal activity; (ii) sequential deletion of three of the negative cis‐acting elements results in a mutated promoter that is 40 times (sucrose broth) or 12 times (lactose broth) more active than the wild type; (iii) one of these negative cis‐acting elements is involved in sucrose repression. Strikingly, it is located outside the non‐transcribed 525 bp intergenic region and maps to the coding region of the divergently transcribed ACVS gene; (iv) a 5′‐del‐etion up to −56 (relative to the major tsp) contains information to provide almost half of the maximal promoter activity and allows initiation of transcription at the correct site. By using total‐protein extracts from mycelia grown under penicillin producing conditions we have detected a DNA‐binding activity that specifically shifts a promoter fragment located between −654 and −455(relative to IPNS tsp). Deletions covering this region partially abolish IPNS promoter activity. The fragment in question overlaps the ACVS tsp.
Gene‐specific translational control of the yeast GCN4 gene by phosphorylation of eukaryotic initiation factor 2
Authors: Hinnebusch Alan G. 
Published: October 2006

SummaryPhosphorylation of the α subunit of eukaryotic initiation factor 2 (elF‐2α) is one of the best‐characterized mechanisms for down‐regulating total protein synthesis in mammalian cells in response to various stress conditions. Recent work indicates that regulation of the GCN4 gene of Saccharomyces cerevisiae by amino acid availability represents a gene‐specific case of translational control by phosphorylation of elF‐2α, Four short open reading frames in the leader of GCN4 mRNA (uORFs) restrict the flow of scanning ribosomes from the cap site to the GCN4 initiation codon. When amino acids are abundant, ribosomes translate the first uORF and reinitiate at one of the remaining uORFs in the leader, after which they dissociate from the mRNA. Under conditions of amino acid starvation, many ribosomes which have translated uORFI fail to reinitiate at uORFs 2‐4 and utilize the GCN4 start codon instead. Failure to reinitiate at uORFs 2‐4 in starved cells results from a reduction in the GTP‐bound form of elF‐2 that delivers charged initiator tRNAiMet to the ribosome. When the levels of elF‐2·GTP·Met‐tRNAiMet ternary complexes are low, many ribosomes will not rebind this critical initiation factor following translation of uORF1 until after scanning past uORF4, but before reaching GCN4. Phosphorylation of elF‐2 by the protein kinase GCN2 decreases the concentration of elF‐2·GTP·Met‐tRNAiMet complexes by inhibiting the guanine nucleotide exchange factor for elF‐2, which is the same mechanism utilized in mammalian cells to inhibit total protein synthesis by phosphorylation of elF‐2.
Control and function of lysyl‐tRNA synthetases: diversity and co‐ordination
Authors: Nakamura Yoshikazu , Ito Koichi 
Published: October 2006

SummaryLysyl‐tRNA synthetases are synthesized from two distinct genes in Escherichia coli, lysS (constitutively) and lysU (inducibly); however, the physiological significance and the differential control mechanism of these two genes have been a long‐standing puzzle. Recent studies have successfully uncovered a significant control mechanism of lysU expression, which involves the leucine‐responsive regulatory protein (Lrp) and a translational enhancer element called‘downstream box'. Moreover, it is likely that there is a mechanism underlying co‐ordinate expression of lysU with other genes outside the leucine‐Lrp regulon under harsh conditions such as low pH and anaerobiosis. A possible mechanism of lysyl‐tRNA synthetase expression and function is reviewed.
Common components in the assembly of type 4 fimbriae, DNA transfer systems, filamentous phage and protein‐secretion apparatus: a general system for the formation of surface‐associated protein complexes
Authors: Hobbs Matthew , Mattick John S. 
Published: October 2006

SummaryThe Pseudomonas aeruginosa genes pilB‐D and pilQ are necessary for the assembly of type 4 fimbriae. Homologues of these genes and of the subunit (pilin) gene have been described in various different bacterial species, but not always in association with type 4 fimbrial biosynthesis and function. Pil‐like proteins are also involved in protein secretion, DNA transfer by conjugation and transformation, and morphogenesis of filamentous bacteriophages. It seems likely that the Pil homologues function in the processing and export of proteins resembling type 4 fimbrial sub‐units, and in their organization into fimbrial‐like structures. These may either be true type 4 fimbriae, or components of protein complexes which act in the transport of macromolecules (DNA or protein) into or out of the cell. Some PilB‐like and PilQ‐like proteins are apparently also involved in the assembly of non‐type 4 polymeric structures (filamentous phage virions and conjugative pili). The diverse studies summarized in this review are providing insight into an extensive infrastructural system which appears to be utilized in the formation of a variety of cell surface‐associated complexes.
The galactose regulon of Escherichia coli
Authors: Weickert Michael J. , Adhya Sankar 
Published: October 2006

SummaryGalactose transport and metabolism in Escherichia coli involves a multicomponent amphibolic pathway. Galactose transport is accomplished by two different galactose‐specific transport systems. At least four of the genes and operons involved in galactose transport and metabolism have promoters containing similar regulatory sequences. These sequences are recognized by at least three regulators, Gal repressor (GalR), Gal isorepressor (GalS) and cAMP receptor protein (CRP), which modulate transcription from these promoters. The negative regulators, GalR and GalS, discriminate between utilization of the high‐affinity (regulated by GalS) and low‐affinity (regulated by GalR) transport systems, and modulate the expression of genes for galactose metabolism in an overlapping fashion. GalS is itself autogenously regulated and CRP dependent, while the gene for GalR is constitutive. The gal operon encoding the enzymes for galactose metabolism has two promoters regulated by CRP in opposite ways; one (P1) is stimulated and the other (P2) inhibited by CRP. Both promoters are strongly repressed by GalR but weakly by GalS. All but one of the constituent promoters of the gal regulon have two operators. The gal regulon has the potential to coordinate galactose metabolism and transport in a highly efficient manner, under a wide variety of conditions of galactose availability.
Identification of genes involved in utilization of acetate and acetoin in Bacillus subtilis
Authors: Grundy Frank J. , Waters Debra A. , Takova Tsetska Y. , Henkin Tina M. 
Published: October 2006

SummaryThe Bacillus subtilis ccpA gene has previously been shown to be involved in repression of amyE expression when cells are grown in excess glucose. The region of the B. subtilis chromosome downstream from ccpA was characterized to determine if additional genes involved in carbohydrate metabolism were present. Two open reading frames that exhibited sequence similarity to the Escherichia coli and B. subtilis motA and motB motility genes were found immediately downstream from ccpA; disruption of this region had no effect on growth, sporulation or motility. Two divergent transcriptional units containing the acsA and acuABC genes were also found in this region. The acsA gene encodes acetyl‐CoA synthetase, and inactivation of this gene resulted in loss of the ability to utilize acetate as a carbon source for growth or sporulation. Disruption of the acuABC genes resulted in poor growth or sporulation on acetoin or butanediol. The acsA and acuABC promoter sequences were identified by primer extension, and are in close proximity. Two sequences resembling the amyO regulatory target site necessary for glucose repression of amyE were identified in the acsA‐acuABC promoter regions.
Linker‐insertion mutagenesis of Pseudomonas aeruginosa outer membrane protein OprF
Authors: Wong Rebecca S. Y. , Jost Helen , Hancock Robert E. W. 
Published: October 2006

SummaryThe oprF gene, expressing Pseudomonas aeruginosa major outer membrane protein OprF, was subjected to semi‐random linker mutagenesis by insertion of a 1.3 kb Hincll kanamycin‐resistance fragment from plasmid pUC4KAPA into multiple blunt‐ended restriction sites in the oprF gene. The kanamycin‐resistance gene was then removed by Pstl digestion, which left a 12 nucleotide pair linker residue. Nine unique clones were identified that contained such linkers at different locations within the oprF gene and were permissive for the production of full‐length OprF variants. In addition, one permissive site‐directed insertion, one non‐permissive insertion and one carboxy‐terminal insertion leading to proteolytic truncation were also identified. These mutants were characterized by DNA sequencing and reactivity of the OprF variants with a bank of 10 OprF‐specific monoclonal antibodies. Permissive clones produced OprF variants that were shown to be reactive with the majority of these monoclonal antibodies, except where the insertion was suspected of interrupting the epitope for the specific monoclonal antibody. In addition, these variants were shown to be 2‐mercaptoethanol modifiable, to be resistant to trypsin cleavage in intact cells and partly cleaved to a high‐molecular‐weight core fragment in outer membranes and, where studied, to be accessible to indirect immunofluorescenee labelling in intact cells by monoclonal antibodies specific for surface epitopes. Based on these data, a revised structural model for OprF is proposed.
The ferric iron‐binding protein of pathogenic Neisseria spp. functions as a periplasmic transport protein in iron acquisition from human transferrin
Authors: Chen Cheng‐Yen , Berish Sally A. , Morse Stephen A. , Mietzner Timothy A. 
Published: October 2006

SummaryThe ferric iron‐binding protein (Fbp) expressed by pathogenic Neisseria spp. has been proposed to play a central role in the high‐affinity acquisition of iron from human transferrin. The results of this investigation provide evidence that Fbp participates in this process as a functional analogue of a Gram‐negative periplasmic‐binding protein component, which operates as a part of a general active transport process for the receptor‐mediated, high‐affinity transport of iron from human transferrin. Known properties of Fbp are correlated with those of other well‐characterized periplasmic‐binding proteins, including structural features and the reversible binding of ligand. Predictive of a periplasmic‐binding protein, which functions in the high‐affinity acquisition of iron, is that Fbp is a transient participant in the process of iron acquisition from human transferrin. Evidence for this is demonstrated by results of pulse–chase experiments. Taken together, the data described here and elsewhere suggest that pathogenic Neisseria spp. use a periplasmic‐binding protein‐mediated active transport mechanism for the acquisition of iron from human transferrin.
Homology between a genetic locus (mdoA) involved in the osmoregulated biosynthesis of periplasmic glucans in Escherichia coli and a genetic locus (hrpM) controlling pathogenicity of Pseudomonas syringae
Authors: Loubens I. , Debarbieux L. , Bohin A. , Lacroix J.‐M. , Bohin J.‐P. 
Published: October 2006

SummaryMembrane‐derived oligosaccharides (MDO) of Escherichia coli are representative members of a family of glucans found in the periplasmic space of Gram‐negative bacteria. The two genes forming the mdoGH operon are necessary for the synthesis of MDO. The nucleotide sequence (4759 bp) and the transcription‐al start of this operon were determined. Both gene products were further characterized by gene fusion analysis. MdoG is a 56 kDa periplasmic protein whose function remains to be determined. MdoH, whose presence was shown to be necessary for normal glucosyl transferase activity, is a 97 kDa protein spanning the cytoplasmic membrane. To our surprise, these proteins are not homologous to the periplasmic glucan biosynthetic enzymes previously characterized in the Rhizobiaceae family. However, a considerable homology (69% identical nucleotides out of 2816) was discovered between mdoGH and the two genes present at the hrpM locus of the phytopathogenic bacterium Pseudomonas syringae pv. syringae. Functions of these genes remain mysterious but they are known to be required for both the expression of disease symptoms on host plants and the development of the hypersensitive reaction on non‐host plants (Mills and Mukhopadhyay, 1990). These results confirm the importance of periplasmic glucans for the physiological ecology of Gram‐negative bacteria.
A lowered concentration of cAMP receptor protein caused by glucose is an important determinant for catabolite repression in Escherichia coli
Authors: Ishizuka Hitoshi , Hanamura Akemi , Kunimura Tadashi , Aiba Hiroji 
Published: October 2006

SummaryA decreased intracellular concentration of cAMP is insufficient to account for catabolite repression in Escherichia coli. We show that glucose lowers the amount of cAMP receptor protein (CRP) in cells. A correlation exists between CRP and β‐galactosidase levels in cells growing under various conditions. Exogenous cAMP completely eliminates catabolite repression in CRP‐overproducing cells, while it does not fully reverse the effect of glucose on β‐galactosidase expression in wild‐type cells. When the CRP concentration is reduced by manipulating the crp gene, β‐galactosidase expression decreases in proportion to the concentration of CRP. These findings indicate that the lowered concentration of CRP caused by glucose is one of the major factors for catabolite repression. We propose that glucose causes catabolite repression by lowering the intracellular levels of both CRP and cAMP.
Resistance to nodulation of cv. Afghanistan peas is overcome by nodX, which mediates an O‐acetylation of the Rhizobium leguminosarum lipo‐oligosaccharide nodulation factor
Authors: Firmin J. L. , Wilson K. E. , Carlson R. W. , Davies A. E. , Downie J. A. 
Published: October 2006

SummaryOnly some strains of Rhizobium leguminosarum biovar viciae can efficiently nodulate varieties of peas such as cv. Afghanistan, which carry a recessive allele that blocks efficient nodulation by most western isolates of R. I. viciae. One strain (TOM) which can nodulate cv. Afghanistan peas has a gene (nodX) that is required to overcome the nodulation resistance. Strain TOM makes significantly lower amounts of lipo‐oligosaccharide nodulation factors than other strains of R. I. viciae. and this effect appears to be due to lower levels of nod gene induction. These nodulation factors are similar to those from other R. I. viciae. strains in that they consist of an oligomer of four or five β1‐4‐linked N‐acetylglucosamine residues in which the terminal non‐reducing glucosamine carries an O‐acetyl group and a C18:4 or C18:1N‐acyl group. However, one of the nodulation factors made by strain TOM differs from the factors made by other strains of R. I. viciae. in that it carries an O‐acetyl group on the C‐6 of the reducing N‐acetylglucosamine residue. This acetylation is NodX‐dependent and the pentameric nodulation factor is acetylated on the reducing N‐acetylglucosamine residue whereas the tetrameric nodulation factor is not. Although the nodL gene product is also an O‐acetyl transferase (it O‐acetylates the C‐6 of the terminal non‐reducing glucosamine), there is very little similarity between the amino acid sequences of these two acetyl transferases.
Cloning and molecular analysis of the galE gene of Neisseria meningitidls and its role in lipopolysaccharide biosynthesis
Authors: Jennings Michael P. , van der Ley Peter , Wilks Kathy E. , Maskell Duncan J. , Poolman Jan T. , Moxon E. Richard 
Published: October 2006

SummaryThe galE gene from Haemophilus influenzae was used as a hybridization probe for the galE gene of Neisseria meningitidis Group B, identifying two different homologous loci. Each of the loci was cloned and nucleotide sequence analysis revealed that both loci contained sequences similar to galE. One contained a functional galE gene and mapped to the capsule biosynthetic locus. The second contained only a partial galE‐coding sequence, which did not express a functional gene product. A galE mutant meningococcal strain was constructed by transformation with an inactivated galE gene. Analysis of the LPS from the galE mutant strain revealed an apparent reduction in molecular weight and a loss of reactivity with monoclonal antibodies specific for structures known to contain galactose. These results are consistent with an essential role for galE in the incorporation of galactose into meningococcal lipopolysaccharide.
Regulatory implications of translational frameshifting in cellular gene expression
Authors: Engelberg‐Kulka Hanna , Schoulaker‐Schwarz Rachel 
Published: October 2006

SummaryThe genetic code, once thought to be rigid, hag been found to be quite fiexible, permitting several different reading alternatives. One of these is translatlonal frameshifting, a process programmed in the mRNA sequence and which enables a +1 or ‐1 shift from the reading frame of the initiation codon. So far, the Involvement of translatlonal frameahifting in gene expression has been described mainly in viruses (particularly retroviruses), retrotransposons, and bacterial insertion elements, in this MicroReview., we present a survey of the cellular genes, mostly in Escherichia coil, which have been found to be expressed through a transiational frameshifting process, as well as a discussion of the regulatory implications of this process.
Mammalian and Escherichia coli signal recognition particles
Authors: Luirink Joen , Dobberstein Bernhard 
Published: October 2006

SummaryRecent evidence from both biochemical and genetic studies indicates that protein targeting to the pro‐karyotic cytoplasmic membrane and the eukaryotic endoplasmic reticulum membrane may have more in common than previously thought. A ribonucleo‐protein particle was identified in Escherichia coli that consists of at least one protein (P48 or Ffh) and one RNA molecule (4.5S RNA), both of which exhibit strong sequence similarity with constituents of the mammalian signal recognition particle (SRP). Like the mammalian SRP, the E. coli SRP binds specifically to the signal sequence of presecretory proteins. Depletion of either P48 or 4.5S RNA affects translation and results in the accumulation of precursors of several secreted proteins. This review discusses these recent studies and speculates on the position of the SRP in the complex network of protein interactions involved in translation and membrane targeting in E. coli.
Clonal spread of serogroup A meningococci: a paradigm for the analysis of microevolution in bacteria
Authors: Achtman Mark 
Published: October 2006

SummaryExtensive epidemiological analyses of epidemics of meningococcal meningitis have resulted in large, well‐defined strain collections which represent the local diversity and global spread of serogroup A bacteria. Several genes for cell surface proteins are conserved during spread, with a few exceptions: analysis of these exceptions has revealed some of the phenomena which can lead to microevolution. Micro‐evolution is so rapid with serogroup A meningococcal that several independent recombination events have been documented within the last few decades. In a few cases, the recombinant bacteria have become established by clonal replacement plus epidemic spread. Comparison with other bacteria indicates that serogroup A meningococcal provide a number of advantages for analysis of microevolution.
Identification and characterization of a chromosomal virulence gene, vacJ, required for intercellular spreading of Shigella flexneri
Authors: Suzuki T. , Murai T. , Fukuda I. , Tobe T. , Yoshikawa M. , Sasakawa C. 
Published: October 2006

SummaryIntercellular spreading of shigellae Is a prerequisite for shigellosis, although the molecular mechanisms underlying the phenomenon are still largely obscure. To elucidate some of these mechanisms, we performed random TniO insertion mutagenesis in Shigella flexneri YSH6000T and found a chromosomal locus in the Notl‐J segment responsible for bacterial spreading. The locus affected in the mutant, designated vacJ, was neither involved in the invasion of epithelial cells nor in intracellular movement, but was required for intercellular spread. The vacJ mutant was capable of forming bacterium‐containing membranous protrusions within the infected cell, but had diminished ability to move from the protrusions into the cytoplasm of the adjacent epithelial cells. Cloning and sequencing of the vacJ region Indicated that the vacJ gene encoded a 28.0 kDa protein possessing a signal peptide at the N‐terminus, which contained the motif characteristic of lipoproteins. The analysis of the vacJ product indicated that VacJ was exposed on the bacterial surface. The vacJ gene was distributed among shigellae and enteroinvasive Escherichia coli, and the constructed vacJ mutants failed to spread intercellularly, indicating that vacJ is a chromosomal gene essential for the pathogenicity of shigeiiae.