bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of a novel gene and beta-galactosidase isozyme from a psychrotrophic Arthrobacter isolate
Authors: Gutshall K R , Trimbur D E , Kasmir J J , Brenchley J E
Published: November 2016

We have characterized a new psychrotrophic Arthrobacter isolate which produces beta-galactosidase isozymes. When DNA from this isolate was transformed into an Escherichia coli host, we obtained three different fragments, designated 12, 14, and 15, each encoding a different beta-galactosidase isozyme. The beta-galactosidase produced from fragment 12 was of special interest because the protein subunit was smaller (about 71 versus 116 kDa) than those typically encoded by the lacZ family. The isozyme encoded by fragment 12 was purified, and its activity and thermostability were examined. Although the enzyme is highly specific towards beta-D-galactoside substrates, its levels in the isolate do not increase in cells grown with lactose. Nucleotide sequence determination showed that the gene encoding isozyme 12 is not similar to the other members of the lacZ family but has regions similar to beta-galactosidase isozymes from Bacillus stearothermophilus and B. circulans. Addition of the isozyme 12 sequence to the database made it possible to examine these enzymes as possible members of a new, separate family. Our analysis of this new family showed some conserved amino acids corresponding to the lacZ acid-base catalytic region but no homology with the nucleophilic region. On the basis of these comparisons, we designated this a new lacG family.
Mechanisms of biodegradation of metal-citrate complexes by Pseudomonas fluorescens
Authors: Joshi-Tope G , Francis A J
Published: November 2016

Biodegradation of metal-citrate complexes by Pseudomonas fluorescens depends on the nature of the complex formed between the metal and citric acid. Bidentate Fe(III)-, Ni-, and Zn-citrate complexes were readily biodegraded, but the tridentate Cd- and Cu-citrate, and U-citrate complexes were not. The biodegradation of Ni- and Zn-citrate commenced after an initial lag period; the former showed only partial (70%) degradation, whereas the latter was completely degraded. Uptake studies with 14C-labeled citric acid and metal-citrate complexes showed that cells grown in medium containing citric acid transported free citric acid at the rate of 28 nmol min-1 and Fe(III)-citrate at the rate of 12.6 nmol min-1 but not Cd-, Cu-, Ni-, U-, and Zn-citrate complexes. However, cells grown in medium containing Ni- or Zn-citrate transported both Ni- and Zn-citrate, suggesting the involvement of a common, inducible transport factor. Cell extracts degraded Fe(III)-, Ni-, U-, and Zn-citrate complexes in the following order: The cell extract did not degrade Cd- or Cu-citrate complexes. These results show that the biodegradation of the U-citrate complex was limited by the lack of transport inside the cell and that the tridentate Cd- and Cu-citrate complexes were neither transported inside the cell nor metabolized by the bacterium.
Genes encoded on a cyanobacterial plasmid are transcriptionally regulated by sulfur availability and CysR
Authors: Nicholson M L , Laudenbach D E
Published: November 2016

A cyanobacterial sulfur-regulated gene (cysR), which encodes a protein with similarity to the Crp family of prokaryotic regulatory proteins, has recently been isolated and characterized. Polyacrylamide gel electrophoresis of periplasmic protein extracts reveals that a cysR mutant fails to synthesize a 36-kDa polypeptide that is normally induced in wild-type cells that have been grown under sulfur-deficient conditions. The amino-terminal sequence of this protein was obtained, and a synthetic oligonucleotide was used to isolated a clone containing a 1.9-kb NruI-KpnI fragment from a Synechococcus sp. strain PCC 7942 genomic library. RNA blot analysis indicates that this fragment encodes a transcript that is detectable in wild-type but not cysR mutant cells that have been starved for sulfur. DNA blot analysis revealed that the 1.9-kb NruI-KpnI fragment is contained within the Ba4 BamHI fragment of the endogenous 50-kb plasmid pANL. RNA blot studies indicate that the accumulation of a large number of pANL transcripts is regulated by sulfur levels and CysR. DNA sequence analysis confirmed that the gene encoding the sulfur-regulated 36-kDa periplasmic protein is encoded on the Ba4 fragment of pANL. The sequence of the 36-kDa protein displays sequence similarity to the enzyme catalase, and two downstream proteins exhibit 25 and 62% identity to a subunit of a P-type ATPase complex involved in Mg2+ transport and a chromate resistance determinant, respectively. Surprisingly, a strain in which the putative chromate resistance gene was interrupted by a drug resistance marker exhibited increased resistance to chromate when grown in media containing low sulfate concentrations. The possible role of this protein in the acclimation of cyanobacteria to conditions of low sulfur availability is discussed.
An extracellular factor regulates expression of sdiA, a transcriptional activator of cell division genes in Escherichia coli
Authors: García-Lara J , Shang L H , Rothfield L I
Published: November 2016

The sdiA gene codes for a protein that regulates expression of the ftsQAZ cluster of essential cell division genes of Escherichia coli. SdiA up-regulates the ftsQ2p promoter that initiates transcription into the ftsQAZ cluster. In this paper, we report that expression of sdiA is itself regulated by a factor that is released into the growth medium by E. coli. When medium that had previously supported growth of E. coli (conditioned medium) was used to support growth of an indicator E. coli strain that contained an sdiA-lacZ transcriptional reporter, there was a 50 to 80% decrease in sdiA expression as monitored by beta-galactosidase activity. The down-regulation of PsdiA was associated with a decrease in expression of the SdiA target promoter ftsQ2p, as monitored by expression of an ftsQ2p-lacZ transcriptional fusion. An effect of conditioned medium on ftsQ2p expression was not seen when the wild-type sdiA gene was disrupted by insertional mutagenesis, indicating that the effect on ftsQ2p expression was secondary to the down-regulation of PsdiA. Conditioned medium had no effect on expression of Plac, PrpoS, or several other promoters associated with the ftsQAZ gene cluster (ftsQ1p and ftsZ1-4p). This suggests that the response is specific for PsdiA and for promoters that are regulated by the sdiA gene product and that cell-to-cell signalling may play a role in regulating expression of this group of genes.
Analysis of 0.5-kilobase-pair repeats in the Mycoplasma hominis lmp gene system and identification of gene products
Authors: Ladefoged S A , Jensen L T , Brock B , Birkelund S , Christiansen G
Published: November 2016

Mycoplasma hominis, an opportunistic pathogenic bacterium of humans, has a small genome of 700 kb. Despite this, multiple copies of gene sequences with similarities to the structural gene (lmp1) of a 135-kDa surface-located membrane protein (Lmp1) have been identified on the genome of M. hominis PG21 (lmp2, lmp3, and lmp4). The distance between the lmp1-lmp2 region and the lmp3-lmp4 region was more than 110 kb. lmp3-lmp4 of M. hominis PG21 was sequenced and found to contain two putative genes. The gene region of 6.5 kb contained a 5' unique region and a 3' unique region separated by 9 0.5-kb repeats with 51 to 90% similarity to 10 similar repeats found in the lmp1-lmp2 region. The 0.5-kb DNA repeats thus comprised about 1% of the entire genome. In both regions, a base change in one of the repeats gave rise to a stop codon, and thereby lmp2 and lmp4 occurred. By PCR amplification of reverse-transcriptase-generated cDNA it was shown that all four genes were transcribed. By use of Lmp-specific antibodies we showed that both lmp1 and lmp3 were translated into proteins (Lmp1 and Lmp3). Each of the four lmp genes represented by their unique cloned segments was used as a probe to analyze the presence, distribution, and organization of the genes within the genome in 13 M. hominis isolates. The repetitive element was detected at one or two locations on the chromosome for all isolates. The lmp3-specific element was present in all isolates, and lmp1- and lmp2-specific elements were present in all but one isolate. The lmp4-specific element was present in about half the isolates tested. For five M. hominis isolates the chromosomal location of the lmp genes was mapped.
Analysis of the role of prespore gene expression in the compartmentalization of mother cell-specific gene expression during sporulation of Bacillus subtilis
Authors: Zhang L , Higgins M L , Piggot P J , Karow M L
Published: November 2016

A hallmark of sporulation of Bacillus subtilis is the formation of two distinct cells by an asymmetric division. The development programs in these two cells involve the compartmentalized activities of sigma E in the larger mother cell and of sigma F in the smaller prespore. Activation of sigma E requires expression of the sigma F-directed gene spoIIR. By immunofluorescence microscopy of a strain containing a spoIIR-lacZ fusion, we have shown that spoIIR is transcribed exclusively in the prespore. By placing spoIIR under the control of PspoIIE, it was possible to express spoIIR before the spore septum was formed. Strains containing the PspoIIE-spoIIR construct activated sigma E only in the mother cell in organisms that underwent the asymmetric sporulation division. Thus, compartmentalization of sigma E activity did not require the compartmentalization of spoIIR expression. Nor did the compartmentalization of sigma E require SpoIIAA, SpoIIAB, sigma F, or sigma F-dependent transcription, all of which are required for prespore-specific gene expression. It is inferred that although sigma F and sigma E direct compartmentalized gene expression, neither of these sigma factors, nor the genes under their control, directs the process of compartmentalization.
Purification of a novel coenzyme F420-dependent glucose-6-phosphate dehydrogenase from Mycobacterium smegmatis
Authors: Purwantini E , Daniels L
Published: November 2016

A variety of Mycobacterium species contained the 5-deazaflavin coenzyme known as F420. Mycobacterium smegmatis was found to have a glucose-6-phosphate dehydrogenase that was dependent on F420 as an electron acceptor and which did not utilize NAD or NADP. The enzyme was purified by ammonium sulfate fractionation, phenyl-Sepharose column chromatography, F420-ether-linked aminohexyl-Sepharose 4B affinity chromatography, and quaternary aminoethyl-Sephadex column chromatography, and the sequence of the first 26 N-terminal amino acids has been determined. The response of enzyme activity to a range of pHs revealed a two-peak pattern, with maxima at pH 5.5 and 8.0. The apparent Km values for F420 and glucose-6-phosphate were, respectively, 0.004 and 1.6 mM. The apparent native and subunit molecular masses were 78,000 and approximately 40,000 Da, respectively.
Construction and characterization of two lexA mutants of Salmonella typhimurium with different UV sensitivities and UV mutabilities
Authors: Clerch B , Garriga X , Torrents E , Rosales C M , Llagostera M
Published: November 2016

Salmonella typhimurium has a SOS regulon which resembles that of Escherichia coli. recA mutants of S. typhimurium have already been isolated, but no mutations in lexA have been described yet. In this work, two different lexA mutants of S. typhimurium LT2 have been constructed on a sulA background to prevent cell death and further characterized. The lexA552 and lexA11 alleles contain an insertion of the kanamycin resistance fragment into the carboxy- and amino-terminal regions of the lexA gene, respectively. SOS induction assays indicated that both lexA mutants exhibited a LexA(Def) phenotype, although SOS genes were apparently more derepressed in the lexA11 mutant than in the lexA552 mutant. Like lexA(Def) of E. coli, both lexA mutations only moderately increased the UV survival of S. typhimurium, and the lexA552 strain was as mutable as the lexA+ strain by UV in the presence of plasmids encoding MucAB or E. coli UmuDC (UmuDCEc). In contrast, a lexA11 strain carrying any of these plasmids was nonmutable by UV. This unexpected behavior was abolished when the lexA11 mutation was complemented in trans by the lexA gene of S. typhimurium. The results of UV mutagenesis correlated well with those of survival to UV irradiation, indicating that MucAB and UmuDCEc proteins participate in the error-prone repair of UV damage in lexA552 but not in lexA11. These intriguing differences between the mutagenic responses of lexA552 and lexA11 mutants to UV irradiation are discussed, taking into account the different degrees to which the SOS response is derepressed in these mutants.
Characterization of the primary immunity region of the Escherichia coli linear plasmid prophage N15
Authors: Lobocka M B , Svarchevsky A N , Rybchin V N , Yarmolinsky M B
Published: November 2016

N15 is the only bacteriophage of Escherichia coli known to lysogenize as a linear plasmid. Clear-plaque mutations lie in at least two regions of the 46-kb genome. We have cloned, sequenced, and characterized the primary immunity region, immB. This region contains a gene, cB, whose product shows homology to lambdoid phage repressors. The cB3 mutation confers thermoinducibility on N15 lysogens, consistent with CB being the primary repressor of N15. Downstream of cB lies the locus of N15 plasmid replication. Upstream of cB lies an operon predicted to encode two products: one homologous to the late repressor of P22 (Cro), the other homologous to the late antiterminator of phi 82 (Q). The Q-like protein is essential for phage development. We show that CB protein regulates the expression of genes that flank the cB gene by binding to DNA at symmetric 16-bp sites. Three sites are clustered upstream of cB and overlap a predicted promoter of the cro and Q-like genes as well as two predicted promoters of cB itself. Two sites downstream of cB overlap a predicted promoter of a plasmid replication gene, repA, consistent with the higher copy number of the mutant, N15cB3. The leader region of repA contains terminators in both orientations and a putative promoter. The organization of these regulatory elements suggests that N15 plasmid replication is controlled not only by CB but also by an antisense RNA and by a balance between termination and antitermination.
Site-specific proteolysis of the Escherichia coli SecA protein in vivo
Authors: Mondigler M , Ehrmann M
Published: November 2016

A seven-amino-acid cleavage site specific for tobacco etch virus (TEV) protease was introduced into SecA at two separate positions after amino acids 195 and 252. Chromosomal wild-type secA was replaced by these secA constructs. Simultaneous expression of TEV protease led to cleavage of both SecA derivatives. In the functional SecA dimer, proteolysis directly indicated surface exposure of the TEV protease cleavage sites. Cleavage of SecA near residue 195 generated an unstable proteolysis product and a secretion defect, suggesting that this approach could be used to inactivate essential proteins in vivo.
Cloning and characterization of CSP37, a novel gene encoding a putative membrane protein of Candida albicans
Authors: Sentandreu M , Nieto A , Iborra A , Elorza M V , Ponton J , Fonzi W A , Sentandreu R
Published: November 2016

In the course of an analysis of the functions and assembly of the cell wall of Candida albicans, we have cloned and characterized a gene, which we designated CSP37 (cell surface protein), encoding a 37-kDa polypeptide which is a membrane-associated protein. The gene was isolated by immunological screening of a DNA library constructed from mycelial cells with a polyclonal serum raised against cell walls of this morphology. Analysis of the nucleotide sequence of a corresponding genomic DNA fragment revealed a single open reading frame which encodes a predicted protein of 321 amino acids with no significant homology to others in the databases. Disruption of the CSP37 gene by the method described by Fonzi and Irwin (Genetics 134:717-728, 1993) eliminated expression of the Csp37 protein. The mutant strains showed no apparent defect in cell viability, growth, or cell wall assembly but displayed attenuated virulence in systemic infections induced in mice and reduced the ability to adhere to polystyrene.
Involvement of NtcB, a LysR family transcription factor, in nitrite activation of the nitrate assimilation operon in the cyanobacterium Synechococcus sp. strain PCC 7942
Authors: Aichi M , Omata T
Published: November 2016

Nitrite, either exogenously supplied or endogenously generated by nitrate reduction, activates transcription of the nitrate assimilation operon (nirA-nrtABCD-narB) in Synechococcus sp. strain PCC 7942 cells treated with L-methionine-DL-sulfoximine (an inhibitor of glutamine synthetase), in which there is no negative feedback resulting from fixation of the ammonium generated by nitrite reduction (Kikuchi et al., J. Bacteriol. 178:5822-5825, 1996). Other transcription units related to nitrogen assimilation, i.e., the nirB-ntcB operon, glnA, and ntcA, were not activated by nitrite. Nitrite did not activate nirA operon transcription in a mutant with a deletion of ntcB, an ammonium-repressible gene encoding a LysR-type DNA-binding protein. Introduction of plasmid-borne ntcB into the ntcB deletion mutant restored the response of the cells to nitrite, indicating that NtcB activates the nirA operon in response to nitrite. Supplementation of nitrite or nitrate to nitrogen-starved cultures of the wild-type strain, but not of the ntcB deletion mutant, caused activation of the nirA operon without L-methionine-DL-sulfoximine treatment of the cells. The results suggested that the positive-regulation mechanism of nirA operon transcription plays a role in rapid adaptation of nitrogen-starved cells to changing availability of nitrate and nitrite.
Adaptation of metabolic enzyme activities of Trypanosoma brucei promastigotes to growth rate and carbon regimen
Authors: ter Kuile B H
Published: November 2016

The insect stage of Trypanosoma brucei adapted the activities of 16 metabolic enzymes to growth rate and carbon source. Cells were grown in chemostats with glucose, rate limiting or in excess, or high concentrations of proline as carbon and energy sources. At each steady state, samples were collected for measurements of substrate and end product concentrations, cellular parameters, and enzyme activities. Correlation coefficients were calculated for all parameters and used to analyze the data set. Rates of substrate consumption and end product formation increased with increasing growth rate. Acetate and succinate were the major nonvolatile end products, but measurable quantities of alanine were also produced. More acetate than succinate was formed during growth on glucose, but growth on proline yielded an equimolar ratio. Growth rate barely affected the relative amounts of end products formed. The end products accounted for the glucose consumed during glucose-limited growth and growth at high rates on excess glucose. A discrepancy, indicating production of CO2, occurred during slow growth on excess glucose and, even more pronounced, in cells growing on proline. The activities of the metabolic enzymes varied by factors of 2 to 40. There was no single enzyme that correlated with consumption of substrate and/or end product formation in all cases. A group of enzymes whose activities rigorously covaried could also not be identified. These findings indicate that T. brucei adapted the activities of each of the metabolic enzymes studied separately. The results of this complex manner of adaptation were more or less constant ratios of the end products and a very efficient energy metabolism.
Identification and functional characterization of an ABC transport system involved in polysaccharide export of A-band lipopolysaccharide in Pseudomonas aeruginosa
Authors: Rocchetta H L , Lam J S
Published: November 2016

Pseudomonas aeruginosa coexpresses two distinct lipopolysaccharide (LPS) molecules known as A band and B band. B band is the serospecific LPS, while A band is the common LPS antigen composed of a D-rhamnose O-polysaccharide region. An operon containing eight genes responsible for A-band polysaccharide biosynthesis and export has recently been identified and characterized (H. L. Rocchetta, L. L. Burrows, J. C. Pacan, and J. S. Lam, unpublished data; H. L. Rocchetta, J. C. Pacan, and J. S. Lam, unpublished data). In this study, we report the characterization of two genes within the cluster, designated wzm and wzt. The Wzm and Wzt proteins have predicted sizes of 29.5 and 47.2 kDa, respectively, and are homologous to a number of proteins that comprise ABC (ATP-binding cassette) transport systems. Wzm is an integral membrane protein with six potential membrane-spanning domains, while Wzt is an ATP-binding protein containing a highly conserved ATP-binding motif. Chromosomal wzm and wzt mutants were generated by using a gene replacement strategy in P. aeruginosa PAO1 (serotype 05). Western blot analysis and immunoelectron microscopy using A-band- and B-band-specific monoclonal antibodies demonstrated that the wzm and wzt mutants were able to synthesize A-band polysaccharide, although transport of the polymer to the cell surface was inhibited. The inability of the polymer to cross the inner membrane resulted in the accumulation of cytoplasmic A-band polysaccharide. This A-band polysaccharide is likely linked to a carrier lipid molecule with a phenol-labile linkage. Chromosomal mutations in wzm and wzt were found to have no effect on B-band LPS synthesis. Rather, immunoelectron microscopy revealed that the presence of A-band LPS may influence the arrangement of B-band LPS on the cell surface. These results demonstrate that A-band and B-band O-antigen assembly processes follow two distinct pathways, with the former requiring an ABC transport system for cell surface expression.
Deletion of the Bacillus subtilis isocitrate dehydrogenase gene causes a block at stage I of sporulation
Authors: Jin S , Levin P A , Matsuno K , Grossman A D , Sonenshein A L
Published: November 2016

A Bacillus subtilis mutant with a deletion of citC, the gene encoding isocitrate dehydrogenase, the third enzyme of the tricarboxylic acid branch of the Krebs cycle, had a greatly reduced ability to sporulate. Analysis of expression of lacZ fusions to various sporulation gene promoters revealed that in the citC mutant development is probably blocked between stage 0 and stage II. That is, genes expressed very early in sporulation, under the direct control of the Spo0A transcription factor, were induced normally in the citC mutant. However, genes expressed after asymmetric septation (stage II) in wild-type cells were not induced in the citC mutant. Analysis of cell morphology by thin-section electron microscopy and immunofluorescence microscopy showed that the mutant formed axial chromosomal filaments and accumulated rings of FtsZ protein at potential polar division sites but failed to form asymmetric division septa, indicating that sporulation is blocked at stage I. The growth and sporulation defects of the B. subtilis citC mutant were fully overcome by introduction and expression of the Escherichia coli icd gene, encoding an isocitrate dehydrogenase similar to the enzyme from B. subtilis.
Identification and characterization of genes encoding carbazole 1,9a-dioxygenase in Pseudomonas sp. strain CA10
Authors: Sato S I , Nam J W , Kasuga K , Nojiri H , Yamane H , Omori T
Published: November 2016

Nucleotide sequence analysis of the flanking regions of the carBC genes of Pseudomonas sp. strain CA10 revealed that there were two open reading frames (ORFs) ORF4 and ORF5, in the upstream region of carBC. Similarly, three ORFs, ORF6 to ORF8, were found in the downstream region of carBC. The deduced amino acid sequences of ORF6 and ORF8 showed homologies with ferredoxin and ferredoxin reductase components of bacterial multicomponent dioxygenase systems, respectively. ORF4 and ORF5 had the same sequence and were tandemly linked. Their deduced amino acid sequences showed about 30% homology with large (alpha) subunits of other terminal oxygenase components. Functional analysis using resting cells harboring the deleted plasmids revealed that the products of ORF4 and -5, ORF6, and ORF8 were terminal dioxygenase, ferredoxin, and ferredoxin reductase, respectively, of carbazole 1,9a-dioxygenase (CARDO), which attacks the angular position adjacent to the nitrogen atom of carbazole, and that the product of ORF7 is not indispensable for CARDO activity. Based on the results, ORF4, ORF5, ORF6, and ORF8 were designated carAa, carAa, carAc, and carAd, respectively. The products of carAa, carAd, and ORF7 were shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis to be polypeptides with molecular masses of 43, 36, and 11 kDa, respectively. However, the product of carAc was not detected in Escherichia coli. CARDO has the ability to oxidize a wide variety of polyaromatic compounds, including dibenzo-p-dioxin, dibenzofuran, biphenyl, and polycyclic aromatic hydrocarbons such as naphthalene and phenanthrene. Since 2,2',3-trihydroxydiphenyl ether and 2,2',3-trihydroxybiphenyl were identified as metabolites of dibenzo-p-dioxin and dibenzofuran, respectively, it was considered that CARDO attacked at the angular position adjacent to the oxygen atom of dibenzo-p-dioxin and dibenzofuran as in the case with carbazole.
Localization and cell surface anchoring of the Saccharomyces cerevisiae flocculation protein Flo1p
Authors: Bony M , Thines-Sempoux D , Barre P , Blondin B
Published: November 2016

The Saccharomyces cerevisiae FLO1 gene encodes a large 1,536-amino-acid serine- and threonine-rich protein involved in flocculation. We have assessed the localization of Flo1p by immunoelectron microscopy, and in this study we show that this protein is located in the external mannoprotein layer of the cell wall, at the plasma membrane level and in the periplasm. The protein was also visualized in the endoplasmic reticulum and in the nuclear envelope, indicating that it was secreted through the secretory pathway. The protein was detected by Western blotting in cell wall extracts as a high-molecular-mass (>200 kDa) polydisperse material obviously as a result of extensive N and probably O glycosylation. Flo1p was extracted from cell walls in large amounts by boiling in sodium dodecyl sulfate, suggesting that it is noncovalently anchored to the cell wall network. The membranous forms of Flo1p were shown to be solubilized by phosphatidylinositol-phospholipase C treatment, suggesting that Flo1p is glycosyl phosphatidylinositol (GPI) anchored to this organelle. The expression of truncated forms with the hydrophobic C-terminal domain deleted led to the secretion of the protein in the culture medium. The hydrophobic C terminus, which is a putative GPI anchoring domain, is therefore necessary for the attachment of Flo1p in the cell wall. Deletion analysis also revealed that the N-terminal domain of Flo1p was essential for cellular aggregation. On the whole, our data indicate that Flo1p is a true cell wall protein which plays a direct role in cell-cell interaction.
Overexpression of the D-alanine racemase gene confers resistance to D-cycloserine in Mycobacterium smegmatis
Authors: Cáceres N E , Harris N B , Wellehan J F , Feng Z , Kapur V , Barletta R G
Published: November 2016

D-Cycloserine is an effective second-line drug against Mycobacterium avium and Mycobacterium tuberculosis. To analyze the genetic determinants of D-cycloserine resistance in mycobacteria, a library of a resistant Mycobacterium smegmatis mutant was constructed. A resistant clone harboring a recombinant plasmid with a 3.1-kb insert that contained the glutamate decarboxylase (gadA) and D-alanine racemase (alrA) genes was identified. Subcloning experiments demonstrated that alrA was necessary and sufficient to confer a D-cycloserine resistance phenotype. The D-alanine racemase activities of wild-type and recombinant M. smegmatis strains were inhibited by D-cycloserine in a concentration-dependent manner. The D-cycloserine resistance phenotype in the recombinant clone was due to the overexpression of the wild-type alrA gene in a multicopy vector. Analysis of a spontaneous resistant mutant also demonstrated overproduction of wild-type AlrA enzyme. Nucleotide sequence analysis of the overproducing mutant revealed a single transversion (G-->T) at the alrA promoter, which resulted in elevated beta-galactosidase reporter gene expression. Furthermore, transformants of Mycobacterium intracellulare and Mycobacterium bovis BCG carrying the M. smegmatis wild-type alrA gene in a multicopy vector were resistant to D-cycloserine, suggesting that AlrA overproduction is a potential mechanism of D-cycloserine resistance in clinical isolates of M. tuberculosis and other pathogenic mycobacteria. In conclusion, these results show that one of the mechanisms of D-cycloserine resistance in M. smegmatis involves the overexpression of the alrA gene due to a promoter-up mutation.
PcaK, a high-affinity permease for the aromatic compounds 4-hydroxybenzoate and protocatechuate from Pseudomonas putida
Authors: Nichols N N , Harwood C S
Published: November 2016

PcaK is a transporter and chemoreceptor protein from Pseudomonas putida that is encoded as part of the beta-ketoadipate pathway regulon for aromatic acid degradation. When expressed in Escherichia coli, PcaK was localized to the membrane and catalyzed the accumulation of two aromatic substrates, 4-hydroxybenzoate and protocatechuate, against a concentration gradient. Benzoate inhibited 4-hydroxybenzoate uptake but was not a substrate for PcaK-catalyzed transport. A P. putida pcaK mutant was defective in its ability to accumulate micromolar amounts of 4-hydroxybenzoate and protocatechuate. The mutant was also impaired in growth on millimolar concentrations of these aromatic acids. In contrast, the pcaK mutant grew at wild-type rates on benzoate. The Vmax for uptake of 4-hydroxybenzoate was at least 25 nmol/min/mg of protein, and the Km was 6 microM. PcaK-mediated transport is energized by the proton motive force. These results show that although aromatic acids in the undissociated (uncharged) form can diffuse across bacterial membranes, high-specificity active transport systems probably also contribute to the ability of bacteria to grow on the micromolar concentrations of these compounds that are typically present in soil. A variety of aromatic molecules, including naturally occurring lignin derivatives and xenobiotics, are metabolized by bacteria and may be substrates for transport proteins. The characterization of PcaK provides a foundation for understanding active transport as a critical step in the metabolism of aromatic carbon sources.
Tromp1, a putative rare outer membrane protein, is anchored by an uncleaved signal sequence to the Treponema pallidum cytoplasmic membrane
Authors: Akins D R , Robinson E , Shevchenko D , Elkins C , Cox D L , Radolf J D
Published: November 2016

Treponema pallidum rare outer membrane protein 1 (Tromp1) has extensive sequence homology with substrate-binding proteins of ATP-binding cassette transporters. Because such proteins typically are periplasmic or cytoplasmic membrane associated, experiments were conducted to clarify Tromp1's physicochemical properties and cellular location in T. pallidum. Comparison of the sodium dodecyl sulfate-polyacrylamide gel electrophoresis mobilities of (i) native Tromp1 and Tromp1 synthesized by coupled in vitro transcription-translation and (ii) native Tromp1 and recombinant Tromp1 lacking the N-terminal signal sequence revealed that the native protein is not processed. Other studies demonstrated that recombinant Tromp1 lacks three basic porin-like properties: (i) the ability to form aqueous channels in liposomes which permit the influx of small hydrophilic solutes, (ii) an extensive beta-sheet secondary structure, and (iii) amphiphilicity. Subsurface localization of native Tromp1 was demonstrated by immunofluorescence analysis of treponemes encapsulated in gel microdroplets, while opsonization assays failed to detect surface-exposed Tromp1. Incubation of motile treponemes with 3-(trifluoromethyl)-3-(m-[125I]iodophenyl)-diazarine, a photoactivatable, lipophilic probe, also did not result in the detection of Tromp1 within the outer membranes of intact treponemes but, instead, resulted in the labeling of a basic 30.5-kDa presumptive outer membrane protein. Finally, analysis of fractionated treponemes revealed that native Tromp1 is associated predominantly with cell cylinders. These findings comprise a body of evidence that Tromp1 actually is anchored by an uncleaved signal sequence to the periplasmic face of the T. pallidum cytoplasmic membrane, where it likely subserves a transport-related function.
Transcriptional and mutational analyses of the rpoN operon in Caulobacter crescentus
Authors: Janakiraman R S , Brun Y V
Published: November 2016

The alternative sigma factor sigma54 is required for the biogenesis of both the flagellum and the stalk in Caulobacter crescentus. The DNA sequence downstream of the sigma54 gene (rpoN) has been determined, revealing three open reading frames (ORFs) encoding peptides of 203, 208, and 159 amino acids. ORF208 and ORF159 are homologous to ORFs found downstream of rpoN in other microorganisms. The organization of this region in C. crescentus is similar to that in other bacteria, with the exception of an additional ORF, ORF203, immediately downstream from rpoN. There is a single temporally regulated promoter that drives the expression of both rpoN and ORF203. Promoter probe analysis indicates the presence of another promoter downstream from ORF203 which exhibits a temporal control that is different from that of the rpoN promoter. Mutational analysis was used to address the function of the proteins encoded by these three downstream ORFs. The mutations have no effect on the transcription of previously known sigma54-dependent flagellar promoters except for a slight effect of an ORF159 mutation on transcription of fljK.
Protection of DNA during oxidative stress by the nonspecific DNA-binding protein Dps
Authors: Martinez A , Kolter R
Published: November 2016

Reactive oxygen species can damage most cellular components, but DNA appears to be the most sensitive target of these agents. Here we present the first evidence of DNA protection against the toxic and mutagenic effects of oxidative damage in metabolically active cells: direct protection of DNA by Dps, an inducible nonspecific DNA-binding protein from Escherichia coli. We demonstrate that in a recA-deficient strain, expression of Dps from an inducible promoter prior to hydrogen peroxide challenge increases survival and reduces the number of chromosomal single-strand breaks. dps mutants exhibit increased levels of the G x C-->T x A mutations characteristic of oxidative damage after treatment with hydrogen peroxide. In addition, expression of Dps from the inducible plasmid reduces the frequency of spontaneous G x C-->T x A and A x T-->T x A mutations and can partially suppress the mutator phenotype of mutM (fpg) and mutY alleles. In a purified in vitro system, Dps reduces the number of DNA single-strand breaks and Fpg-sensitive sites introduced by hydrogen peroxide treatment, indicating that the protection observed in vivo is a direct effect of DNA binding by Dps. The widespread conservation of Dps homologs among prokaryotes suggests that this may be a general strategy for coping with oxidative stress.
Characterization of genes for a second Mo-dependent nitrogenase in the cyanobacterium Anabaena variabilis
Authors: Thiel T , Lyons E M , Erker J C
Published: November 2016

Anabaena variabilis ATCC 29413 is a filamentous heterocystous cyanobacterium that fixes nitrogen under a variety of environmental conditions. Under aerobic growth conditions, nitrogen fixation depends upon differentiation of heterocysts and expression of either a Mo-dependent nitrogenase or a V-dependent nitrogenase in those specialized cells. Under anaerobic conditions, a second Mo-dependent nitrogenase gene cluster, nifII, was expressed in vegetative cells long before heterocysts formed. A strain carrying a mutant gene in the nifII cluster did not fix nitrogen under anaerobic conditions until after heterocysts differentiated. The nifII cluster was similar in organization to the nifI cluster that is expressed in heterocysts and that includes nifBSUHDKENXW as well as three open reading frames that are conserved in both cyanobacterial nif clusters.
Predatory Bacteria Attenuate Klebsiella pneumoniae Burden in Rat Lungs
Authors: Shatzkes Kenneth , Singleton Eric , Tang Chi , Zuena Michael , Shukla Sean , Gupta Shilpi , Dharani Sonal , Onyile Onoyom , Rinaggio Joseph , Connell Nancy D. , Kadouri Daniel E.
Published: November 2016

Bdellovibrio bacteriovorusandMicavibrio aeruginosavorusare predatory bacteria that naturally—and obligately—prey on other Gram-negative bacteria, and their use has been proposed as a potential new approach to control microbial infection. The ability of predatory bacteria to prey on Gram-negative human pathogensin vitrois well documented; however, thein vivosafety and efficacy of predatory bacteria have yet to be fully assessed. In this study, we examined whether predatory bacteria can reduce bacterial burden in the lungs in anin vivomammalian system. Initial safety studies were performed by intranasal inoculation of rats with predatory bacteria. No adverse effects or lung pathology were observed in rats exposed to high concentrations of predatory bacteria at up to 10 days postinoculation. Enzyme-linked immunosorbent assay (ELISA) of the immune response revealed a slight increase in inflammatory cytokine levels at 1 h postinoculation that was not sustained by 48 h. Additionally, dissemination experiments showed that predators were efficiently cleared from the host by 10 days postinoculation. To measure the ability of predatory bacteria to reduce microbial burdenin vivo, we introduced sublethal concentrations ofKlebsiella pneumoniaeinto the lungs of rats via intranasal inoculation and followed with multiple doses of predatory bacteria over 24 h. Predatory bacteria were able to reduceK. pneumoniaebacterial burden, on average, by more than 3.0 log10in the lungs of most rats as measured by CFU plating. The work presented here provides further support for the idea of developing predatory bacteria as a novel biocontrol agent.

IMPORTANCEA widely held notion is that antibiotics are the greatest medical advance of the last 50 years. However, the rise of multidrug-resistant (MDR) bacterial infections has become a global health crisis over the last decade. As we enter the postantibiotic era, it is crucial that we begin to develop new strategies to combat bacterial infection. Here, we report one such new approach: the use of predatory bacteria (Bdellovibrio bacteriovorusandMicavibrio aeruginosavorus) that naturally—and obligately—prey on other Gram-negative bacteria. To our knowledge, this is the first study that demonstrated the ability of predatory bacteria to attenuate the bacterial burden of a key human pathogen in anin vivomammalian system. As the prevalence of MDR infections continues to rise each year, our results may represent a shift in how we approach treating microbial infections in the future.
Causes of underpressure in natural CO2 reservoirs and implications for geological storage
Authors: Akhbari Daria , Hesse Marc A.
Published: November 2016

Geological carbon storage has the potential to reduce anthropogenic carbon dioxide emissions, if large volumes can be injected and securely retained. Storage capacity is limited by regional pressure buildup in the subsurface. However, natural CO2 reservoirs in the United States are commonly underpressured, suggesting that natural processes reduce the pressure buildup over time and increase storage security. To identify these processes, we studied Bravo Dome natural CO2 reservoir (New Mexico, USA), where the gas pressure is up to 6.4 MPa below the hydrostatic pressure, i.e., less than 30% of the expected pressure. Here, we show that the dissolution of CO2 into the brine reduces the pressure by 1.02 ± 0.08 MPa, because Bravo Dome is isolated from the ambient hydrologic system. This challenges the assumption that the successful long-term storage of CO2 is limited to open geological formations. We also show that the formation containing the reservoir was already 2.85 ± 2.02 MPa underpressured before CO2 emplacement. This is likely due to the overlying evaporite layer, which prevents recharge. Similar underpressured formations below regional evaporites are widespread in the midcontinent of the United States. This suggests the existence of significant storage capacities with properties similar to Bravo Dome, which has contained large volumes of CO2 over millennial time scales.
Biomineralization and global change: A new perspective for understanding the end-Permian extinction
Authors: Garbelli Claudio , Angiolini Lucia , Shen Shu-zhong
Published: November 2016

We investigated the kill mechanisms of the end-Permian mass extinction by analyzing patterns in biomineralization of marine invertebrates. The microstructures of Upper Permian brachiopod organocarbonate shells show the demise of the production of fabrics with a columnar layer—which has less organic matrix—in favor of more organic-rich shells at the end of Permian. Also, in the 100–120 k.y. interval prior to the Permian-Triassic boundary (PTB), the Rhynchonellata had small calcite structural units (fibers) and thus a higher shell organic content, whereas the Strophomenata were not able to produce smaller units. This suggests that the two classes had a different capacity to cope with environmental change, with the Rhynchonellata being more able to buffer against pH changes and surviving the PTB, whereas the Strophomenata became extinct. The observed trends in biomineralization are similar to the patterns in extant marine invertebrates exposed to increasing pCO2 and decreasing pH, indicating that ocean acidification could have been one of the kill mechanisms of the mass extinction at the PTB.
Aneurysmal wall imaging in a case of cortical superficial siderosis and multiple unruptured aneurysms
Authors: Yalo Bertrand , Pop Raoul , Zinchenko Ielyzaveta , Diaconu Mihaela , Chibbaro Salvatore , Manisor Monica , Wolff Valerie , Beaujeux Remy
Published: November 2016

We report a case of interhemispheric and bifrontal cortical superficial siderosis in association with two intracranial aneurysms. The patient had no clinical history suggestive of aneurysm rupture, no feature of amyloid angiopathy or other apparent etiology for cortical siderosis. We performed high resolution brain MRI with dark blood T1 sequences before and after IV contrast injection. An anterior communicating aneurysm showed partial wall enhancement on the posterior wall whereas a left posterior communicating aneurysm did not. In the light of recent reports of the association of wall enhancement with unstable aneurysms, we considered wall enhancement to be a marker of inflammation and remodeling of the aneurysm wall, resulting in chronic hemorrhagic suffusion in the subarachnoid spaces. To our knowledge, this is the first report offering proof for a possible link between apparently unruptured aneurysms and cortical siderosis.
Double somatic mutations in mismatch repair genes are frequent in colorectal cancer after Hodgkin's lymphoma treatment
Authors: Rigter Lisanne S , Snaebjornsson Petur , Rosenberg Efraim H , Atmodimedjo Peggy N , Aleman Berthe M , ten Hoeve Jelle , Geurts-Giele Willemina R ,   PALGA group, van Ravesteyn Thomas W , Hoeksel Johan , Meijer Gerrit A , te Riele Hein , van Leeuwen Flora E , Dinjens Winand N , van Leerdam Monique E
Published: November 2016

Objective

Hodgkin's lymphoma survivors who were treated with infradiaphragmatic radiotherapy or procarbazine-containing chemotherapy have a fivefold increased risk of developing colorectal cancer (CRC). This study aims to provide insight into the development of therapy-related CRC (t-CRC) by evaluating histopathological and molecular characteristics.

Design

54 t-CRCs diagnosed in a Hodgkin's lymphoma survivor cohort were analysed for mismatch repair (MMR) proteins by immunohistochemistry, microsatellite instability (MSI) and KRAS/BRAF mutations. MSI t-CRCs were evaluated for promoter methylation and mutations in MMR genes. Pathogenicity of MMR gene mutations was evaluated by in silico predictions and functional analyses. Frequencies were compared with a general population cohort of CRC (n=1111).

Results

KRAS and BRAF mutations were present in 41% and 15% t-CRCs, respectively. Compared with CRCs in the general population, t-CRCs had a higher MSI frequency (24% vs 11%, p=0.003) and more frequent loss of MSH2/MSH6 staining (13% vs 1%, p<0.001). Loss of MLH1/PMS2 staining and MLH1 promoter methylation were equally common in t-CRCs and the general population. In MSI CRCs without MLH1 promoter methylation, double somatic MMR gene mutations (or loss of heterozygosity as second hit) were detected in 7/10 (70%) t-CRCs and 8/36 (22%) CRCs in the general population (p=0.008). These MMR gene mutations in t-CRCs were classified as pathogenic. MSI t-CRC cases could not be ascribed to Lynch syndrome.

Conclusions

We have demonstrated a higher frequency of MSI among t-CRCs, which results from somatic MMR gene mutations. This suggests a novel association of somatic MMR gene mutations with prior anticancer treatment.
Estimating the genetic diversity and structure ofQuercus trojanaWebb populations in Italy by SSRs: implications for management and conservation
Authors: Carabeo Maddalena , Simeone Marco Cosimo , Cherubini Marcello , Mattia Chiara , Chiocchini Francesca , Bertini Laura , Caruso Carla , La Mantia Tommaso , Villani Fiorella , Mattioni Claudia
Published: November 2016

Studying the genetic diversity and structure of the current forest populations is essential for evaluating the ability to survive future biotic and abiotic changes and planning conservation strategies. Quercus trojana Webb is an eastern Mediterranean tree species with a fragmented distribution range, and its westernmost outposts are located in southern Italy. The demand for timber and cropland over the centuries has severely reduced its occurrence in this part of the range. We assessed the genetic diversity and structure of the extant Italian populations of Q. trojana and derived conservation guidelines. A total of 322 samples were genotyped with six polymorphic nuclear microsatellite markers. A high genetic diversity in all populations, two main gene pools, and a highly divergent single population were observed. Based on the allelic richness and heterozygosity estimation, we identified populations that can be considered as valuable source material for conservation programs and those requiring adequate measures to reestablish gene flow and reduce fragmentation. Finally, a comparison with a set of eastern Mediterranean samples indicated a relationship between the Italian and the Greek gene pools. The need to protect these marginal, disjunct populations was further reinforced.