scholarly journals Catabolism of Benzoate and Phthalate in Rhodococcus sp. Strain RHA1: Redundancies and Convergence

2005 ◽  
Vol 187 (12) ◽  
pp. 4050-4063 ◽  
Author(s):  
Marianna A. Patrauchan ◽  
Christine Florizone ◽  
Manisha Dosanjh ◽  
William W. Mohn ◽  
Julian Davies ◽  
...  
Keyword(s):  
Polychlorinated Biphenyl ◽  
Carbon Sources ◽  
Growth Conditions ◽  
Lag Phase ◽  
Gene Products ◽  
Wild Type ◽  
Bacterial Genomes ◽  
Catabolic Genes ◽  
Genes Encoding ◽  
Proteomic Analyses

ABSTRACT Genomic and proteomic approaches were used to investigate phthalate and benzoate catabolism in Rhodococcus sp. strain RHA1, a polychlorinated biphenyl-degrading actinomycete. Sequence analyses identified genes involved in the catabolism of benzoate (ben) and phthalate (pad), the uptake of phthalate (pat), and two branches of the β-ketoadipate pathway (catRABC and pcaJIHGBLFR). The regulatory and structural ben genes are separated by genes encoding a cytochrome P450. The pad and pat genes are contained on a catabolic island that is duplicated on plasmids pRHL1 and pRHL2 and includes predicted terephthalate catabolic genes (tpa). Proteomic analyses demonstrated that the β-ketoadipate pathway is functionally convergent. Specifically, the pad and pat gene products were only detected in phthalate-grown cells. Similarly, the ben and cat gene products were only detected in benzoate-grown cells. However, pca-encoded enzymes were present under both growth conditions. Activity assays for key enzymes confirmed these results. Disruption of pcaL, which encodes a fusion enzyme, abolished growth on phthalate. In contrast, after a lag phase, growth of the mutant on benzoate was similar to that of the wild type. Proteomic analyses revealed 20 proteins in the mutant that were not detected in wild-type cells during growth on benzoate, including a CatD homolog that apparently compensated for loss of PcaL. Analysis of completed bacterial genomes indicates that the convergent β-ketoadipate pathway and some aspects of its genetic organization are characteristic of rhodococci and related actinomycetes. In contrast, the high redundancy of catabolic pathways and enzymes appears to be unique to RHA1 and may increase its potential to adapt to new carbon sources.

Multiple GCD genes required for repression of GCN4, a transcriptional activator of amino acid biosynthetic genes in Saccharomyces cerevisiae

1986 ◽  
Vol 6 (11) ◽  
pp. 3990-3998
Author(s):  
S Harashima ◽  
A G Hinnebusch
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Lacz Gene ◽  
Gene Products ◽  
Wild Type ◽  
Double Mutation ◽  
Double Stranded Rna ◽  
Amino Acid Availability ◽  
Genes Encoding ◽  
New Alleles

GCN4 encodes a positive regulator of multiple unlinked genes encoding amino acid biosynthetic enzymes in Saccharomyces cerevisiae. Expression of GCN4 is coupled to amino acid availability by a control mechanism involving GCD1 as a negative effector and GCN1, GCN2, and GCN3 as positive effectors of GCN4 expression. We used reversion of a gcn2 gcn3 double mutation to isolate new alleles of GCD1 and mutations in four additional GCD genes which we designate GCD10, GCD11, GCD12, and GCD13. All of the mutations lead to constitutive derepression of HIS4 transcription in the absence of the GCN2+ and GCN3+ alleles. By contrast, the gcd mutations require the wild-type GCN4 allele for their derepressing effect, suggesting that each acts by influencing the level of GCN4 activity in the cell. Consistent with this interpretation, mutations in each GCD gene lead to constitutive derepression of a GCN4::lacZ gene fusion. Thus, at least five gene products are required to maintain the normal repressed level of GCN4 expression in nonstarvation conditions. Interestingly, the gcd mutations are pleiotropic and also affect growth rate in nonstarvation conditions. In addition, certain alleles lead to a loss of M double-stranded RNA required for the killer phenotype. This pleiotropy suggests that the GCD gene products contribute to an essential cellular function, in addition to, or in conjunction with, their role in GCN4 regulation.

scholarly journals Genetic and Genomic Insights into the Role of Benzoate-Catabolic Pathway Redundancy in Burkholderia xenovorans LB400

2006 ◽  
Vol 72 (1) ◽  
pp. 585-595 ◽  
Author(s):  
V. J. Denef ◽  
J. A. Klappenbach ◽  
M. A. Patrauchan ◽  
C. Florizone ◽  
J. L. M. Rodrigues ◽  
...  
Keyword(s):  
Polychlorinated Biphenyl ◽  
Gene Clusters ◽  
Large Chromosome ◽  
Wild Type ◽  
Burkholderia Xenovorans ◽  
Burkholderia Xenovorans Lb400 ◽  
Cell Assays ◽  
Aromatic Degradation ◽  
Proteomic Analyses

ABSTRACT Transcriptomic and proteomic analyses of Burkholderia xenovorans LB400, a potent polychlorinated biphenyl (PCB) degrader, have implicated growth substrate- and phase-dependent expression of three benzoate-catabolizing pathways: a catechol ortho cleavage (ben-cat) pathway and two benzoyl-coenzyme A pathways, encoded by gene clusters on the large chromosome (boxC ) and the megaplasmid (boxM ). To elucidate the significance of this apparent redundancy, we constructed mutants with deletions of the ben-cat pathway (the ΔbenABCD::kan mutant), the boxC pathway (the ΔboxABC ::kan mutant), and both pathways (the ΔbenABCDΔ boxABC ::kan mutant). All three mutants oxidized benzoate in resting-cell assays. However, the ΔbenABCD::kan and ΔbenABCD ΔboxABC ::kan mutants grew at reduced rates on benzoate and displayed increased lag phases. By contrast, growth on succinate, on 4-hydroxybenzoate, and on biphenyl was unaffected. Microarray and proteomic analyses revealed that cells of the ΔbenABCD::kan mutant growing on benzoate expressed both box pathways. Overall, these results indicate that all three pathways catabolize benzoate. Deletion of benABCD abolished the ability of LB400 to grow using 3-chlorobenzoate. None of the benzoate pathways could degrade 2- or 4-chlorobenzoate, indicating that the pathway redundancy does not directly contribute to LB400's PCB-degrading capacities. Finally, an extensive sigmaE-regulated oxidative stress response not present in wild-type LB400 grown on benzoate was detected in these deletion mutants, supporting our earlier suggestion that the box pathways are preferentially active under reduced oxygen tension. Our data further substantiate the expansive network of tightly interconnected and complexly regulated aromatic degradation pathways in LB400.

scholarly journals Role of Acinetobacter baylyi Crc in Catabolite Repression of Enzymes for Aromatic Compound Catabolism

2009 ◽  
Vol 191 (8) ◽  
pp. 2834-2842 ◽  
Author(s):  
Tina Zimmermann ◽  
Tobias Sorg ◽  
Simone Yasmin Siehler ◽  
Ulrike Gerischer
Keyword(s):  
Catabolite Repression ◽  
Carbon Sources ◽  
Transcript Abundance ◽  
Growth Conditions ◽  
Wild Type ◽  
Acinetobacter Baylyi ◽  
Transcript Stability ◽  
Key Enzyme ◽  
In The Wild ◽  
First Time

ABSTRACT Here, we describe for the first time the Crc (catabolite repression control) protein from the soil bacterium Acinetobacter baylyi. Expression of A. baylyi crc varied according to the growth conditions. A strain with a disrupted crc gene showed the same growth as the wild type on a number of carbon sources. Carbon catabolite repression by acetate and succinate of protocatechuate 3,4-dioxygenase, the key enzyme of protocatechuate breakdown, was strongly reduced in the crc strain, whereas in the wild-type strain it underwent strong catabolite repression. This strong effect was not based on transcriptional regulation because the transcription pattern of the pca-qui operon (encoding protocatechuate 3,4-dioxygenase) did not reflect the derepression in the absence of Crc. pca-qui transcript abundance was slightly increased in the crc strain. Lack of Crc dramatically increased the mRNA stability of the pca-qui transcript (up to 14-fold), whereas two other transcripts (pobA and catA) remained unaffected. p-Hydroxybenzoate hydroxylase activity, encoded by pobA, was not significantly different in the absence of Crc, as protocatechuate 3,4-dioxygenase was. It is proposed that A. baylyi Crc is involved in the determination of the transcript stability of the pca-qui operon and thereby effects catabolite repression.

scholarly journals Inactivation of an Iron Transporter in Lactococcus lactis Results in Resistance to Tellurite and Oxidative Stress

2007 ◽  
Vol 73 (19) ◽  
pp. 6144-6149 ◽  
Author(s):  
Mark S. Turner ◽  
Yu Pei Tan ◽  
Philip M. Giffard
Keyword(s):  
Oxidative Stress ◽  
Lactococcus Lactis ◽  
Oxygen Toxicity ◽  
Phosphate Transport ◽  
Lag Phase ◽  
Uptake System ◽  
Wild Type ◽  
Oxidative Defense ◽  
Genes Encoding ◽  
Resistant Mutants

ABSTRACT In Lactococcus lactis, the interactions between oxidative defense, metal metabolism, and respiratory metabolism are not fully understood. To provide an insight into these processes, we isolated and characterized mutants of L. lactis resistant to the oxidizing agent tellurite (TeO3 2−), which generates superoxide radicals intracellularly. A collection of tellurite-resistant mutants was obtained using random transposon mutagenesis of L. lactis. These contained insertions in genes encoding a proton-coupled Mn2+/Fe2+ transport homolog (mntH), the high-affinity phosphate transport system (pstABCDEF), a putative osmoprotectant uptake system (choQ), and a homolog of the oxidative defense regulator spx (trmA). The tellurite-resistant mutants all had better survival than the wild type following aerated growth. The mntH mutant was found to be impaired in Fe2+ uptake, suggesting that MntH is a Fe2+ transporter in L. lactis. This mutant is capable of carrying out respiration but does not generate as high a final pH and does not exhibit the long lag phase in the presence of hemin and oxygen that is characteristic of wild-type L. lactis. This study suggests that tellurite-resistant mutants also have increased resistance to oxidative stress and that intracellular Fe2+ can heighten tellurite and oxygen toxicity.

scholarly journals Bacterial Catabolism of β-Hydroxypropiovanillone and β-Hydroxypropiosyringone Produced in the Reductive Cleavage of Arylglycerol-β-Aryl Ether in Lignin

2018 ◽  
Vol 84 (7) ◽  
Author(s):  
Yudai Higuchi ◽  
Shogo Aoki ◽  
Hiroki Takenami ◽  
Naofumi Kamimura ◽  
Kenji Takahashi ◽  
...  
Keyword(s):  
Value Added ◽  
Lignin Biodegradation ◽  
Gene Products ◽  
Aryl Ether ◽  
Ether Linkage ◽  
Content Type ◽  
Catabolic Genes ◽  
Genes Encoding ◽  
Stereospecific Reaction

ABSTRACTSphingobiumsp. strain SYK-6 converts four stereoisomers of arylglycerol-β-guaiacyl ether into achiral β-hydroxypropiovanillone (HPV) via three stereospecific reaction steps. Here, we determined the HPV catabolic pathway and characterized the HPV catabolic genes involved in the first two steps of the pathway. In SYK-6 cells, HPV was oxidized to vanilloyl acetic acid (VAA) via vanilloyl acetaldehyde (VAL). The resulting VAA was further converted into vanillate through the activation of VAA by coenzyme A. A syringyl-type HPV analog, β-hydroxypropiosyringone (HPS), was also catabolized via the same pathway. SLG_12830 (hpvZ), which belongs to the glucose-methanol-choline oxidoreductase family, was isolated as the HPV-converting enzyme gene. AnhpvZmutant completely lost the ability to convert HPV and HPS, indicating thathpvZis essential for the conversion of both the substrates. HpvZ produced inEscherichia colioxidized both HPV and HPS and other 3-phenyl-1-propanol derivatives. HpvZ localized to both the cytoplasm and membrane of SYK-6 and used ubiquinone derivatives as electron acceptors. Thirteen gene products of the 23 aldehyde dehydrogenase (ALDH) genes in SYK-6 were able to oxidize VAL into VAA. Mutant analyses suggested that multiple ALDH genes, including SLG_20400, contribute to the conversion of VAL. We examined whether the genes encoding feruloyl-CoA synthetase (ferA) and feruloyl-CoA hydratase/lyase (ferBandferB2) are involved in the conversion of VAA. Only FerA exhibited activity toward VAA; however, disruption offerAdid not affect VAA conversion. These results indicate that another enzyme system is involved in VAA conversion.IMPORTANCECleavage of the β-aryl ether linkage is the most essential process in lignin biodegradation. Although the bacterial β-aryl ether cleavage pathway and catabolic genes have been well documented, there have been no reports regarding the catabolism of HPV or HPS, the products of cleavage of β-aryl ether compounds. HPV and HPS have also been found to be obtained from lignin by chemoselective catalytic oxidation by 2,3-dichloro-5,6-dicyano-1,4-benzoquinone/tert-butyl nitrite/O2, followed by cleavage of the β-aryl ether with zinc. Therefore, value-added chemicals are expected to be produced from these compounds. In this study, we determined the SYK-6 catabolic pathways for HPV and HPS and identified the catabolic genes involved in the first two steps of the pathways. Since SYK-6 catabolizes HPV through 2-pyrone-4,6-dicarboxylate, which is a building block for functional polymers, characterization of HPV catabolism is important not only for understanding the bacterial lignin catabolic system but also for lignin utilization.

scholarly journals Use of Inducible Feedback-ResistantN-Acetylglutamate Synthetase (argA) Genes for Enhanced Arginine Biosynthesis by Genetically EngineeredEscherichia coli K-12 Strains

1998 ◽  
Vol 64 (5) ◽  
pp. 1805-1811 ◽  
Author(s):  
B. S. Rajagopal ◽  
Joseph DePonte ◽  
Mendel Tuchman ◽  
Michael H. Malamy
Keyword(s):  
Feedback Inhibition ◽  
Expression System ◽  
Point Mutations ◽  
Normal Growth ◽  
Growth Conditions ◽  
Wild Type ◽  
Arginine Biosynthesis ◽  
E Coli ◽  
Genes Encoding ◽  
K 12

ABSTRACT The goal of this work was to construct Escherichia colistrains capable of enhanced arginine production. The arginine biosynthetic capacity of previously engineered E. colistrains with a derepressed arginine regulon was limited by the availability of endogenous ornithine (M. Tuchman, B. S. Rajagopal, M. T. McCann, and M. H. Malamy, Appl. Environ. Microbiol. 63:33–38, 1997). Ornithine biosynthesis is limited due to feedback inhibition by arginine of N-acetylglutamate synthetase (NAGS), the product of the argA gene and the first enzyme in the pathway of arginine biosynthesis in E. coli. To circumvent this inhibition, the argA genes from E. coli mutants with feedback-resistant (fbr) NAGS were cloned into plasmids that contain “arg boxes,” which titrate the ArgR repressor protein, with or without the E. coli carABgenes encoding carbamyl phosphate synthetase and the argIgene for ornithine transcarbamylase. The free arginine production rates of “arg-derepressed” E. coli cells overexpressing plasmid-encoded carAB, argI, and fbr argA genes were 3- to 15-fold higher than that of an equivalent system overexpressing feedback-sensitive wild-type (wt)argA. The expression system with fbr argAproduced 7- to 35-fold more arginine than a system overexpressingcarAB and argI genes on a plasmid in a strain with a wt argA gene on the chromosome. The arginine biosynthetic capacity of arg-derepressed DH5α strains with plasmids containing only the fbr argA gene was similar to that of cells with plasmids also containing the carABand argI genes. Plasmids containing wt or fbrargA were stably maintained under normal growth conditions for at least 18 generations. DNA sequencing identified different point mutations in each of the fbr argA mutants, specifically H15Y, Y19C, S54N, R58H, G287S, and Q432R.

scholarly journals Cephem Potentiation by Inactivation of Nonessential Genes Involved in Cell Wall Biogenesis of β-Lactamase-Producing Escherichia coli

2016 ◽  
Vol 61 (3) ◽  
Author(s):  
Kristin R. Baker ◽  
Helga Høeg Sigurðardóttir ◽  
Bimal Jana ◽  
Luca Guardabassi
Keyword(s):  
Escherichia Coli ◽  
Cell Wall ◽  
Lag Phase ◽  
Growth Curve Analysis ◽  
Wild Type ◽  
Content Type ◽  
Cell Wall Biogenesis ◽  
Genes Encoding ◽  
In The Wild ◽  
Nonessential Genes

ABSTRACT Reversal of antimicrobial resistance is an appealing and largely unexplored strategy in drug discovery. The objective of this study was to identify potential targets for “helper” drugs reversing cephem resistance in Escherichia coli strains producing β-lactamases. A CMY-2-encoding plasmid was transferred by conjugation to seven isogenic deletion mutants exhibiting cephem hypersusceptibility. The effect of each mutation was evaluated by comparing the MICs in the wild type and the mutant harboring the same plasmid. Mutation of two genes encoding proteins involved in cell wall biosynthesis, dapF and mrcB, restored susceptibility to cefoxitin (FOX) and reduced the MICs of cefotaxime and ceftazidime, respectively, from the resistant to the intermediate category according to clinical breakpoints. The same mutants harboring a CTX-M-1-encoding plasmid fell into the intermediate or susceptible category for all three drugs. Individual deletion of dapF and mrcB in a clinical isolate of CTX-M-15-producing E. coli sequence type 131 (ST131) resulted in partial reversal of ceftazidime and cefepime resistance but did not reduce MICs below susceptibility breakpoints. Growth curve analysis indicated no fitness cost in a ΔmrcB mutant, whereas a ΔdapF mutant had a 3-fold longer lag phase than the wild type, suggesting that drugs targeting DapF may display antimicrobial activity, in addition to synergizing with selected cephems. DapF appeared to be a potential FOX helper drug target candidate, since dapF inactivation resulted in synergistic potentiation of FOX in the genetic backgrounds tested. The study showed that individual inactivation of two nonessential genes involved in cell wall biogenesis potentiates cephem activity according to drug- and strain-specific patterns.

scholarly journals sal Genes Determining the Catabolism of Salicylate Esters Are Part of a Supraoperonic Cluster of Catabolic Genes in Acinetobacter sp. Strain ADP1

2000 ◽  
Vol 182 (7) ◽  
pp. 2018-2025 ◽  
Author(s):  
Rheinallt M. Jones ◽  
Vassilis Pagmantidis ◽  
Peter A. Williams
Keyword(s):  
Esterase Activity ◽  
Carbon Sources ◽  
Open Reading Frames ◽  
Fatty Acid Transport ◽  
Gene Products ◽  
Hydroxylase Activity ◽  
Cell Extracts ◽  
Catabolic Genes ◽  
Hydrocarbon Transport ◽  
Reading Frames

ABSTRACT A 5-kbp region upstream of the are-ben-cat genes was cloned from Acinetobacter sp. strain ADP1, extending the supraoperonic cluster of catabolic genes to 30 kbp. Four open reading frames, salA, salR, salE, andsalD, were identified from the nucleotide sequence. Reverse transcription-PCR studies suggested that these open reading frames are organized into two convergent transcription units, salARand salDE. The salE gene, encoding a protein of 239 residues, was ligated into expression vector pET5a. Its product, SalE, was shown to have esterase activity against short-chain alkyl esters of 4-nitrophenol but was also able to hydrolyze ethyl salicylate to ethanol and salicylic acid. A mutant of ADP1 with a Kmrcassette introduced into salE had lost the ability to utilize only ethyl and methyl salicylates of the esters tested as sole carbon sources, and no esterase activity against ethyl salicylate could be detected in cell extracts. SalE was induced during growth on ethyl salicylate but not during growth on salicylate itself. salDencoded a protein of undetermined function with homologies to theEscherichia coli FadL membrane protein, which is involved in facilitating fatty acid transport, and a number of other proteins detected during aromatic catabolism, which may also function in hydrocarbon transport or uptake processes. A Kmr cassette insertion in salD deleteriously affected cell growth and viability. The salA and salR gene products closely resemble two Pseudomonas proteins, NahG and NahR, respectively encoding salicylate hydroxylase and the LysR family regulator of both salicylate and naphthalene catabolism.salA was cloned into pUC18 together with salRand salE, and its gene product showed salicylate-inducible hydroxylase activity against a range of substituted salicylates, with the same relative specific activities as found in wild-type ADP1 grown on salicylate. Mutations involving insertion of Kmrcassettes into salA and salR eliminated expression of salicylate hydroxylase activity and the ability to grow on either salicylate or ethyl salicylate. Studies of mutants with disruptions of genes of the β-ketoadipate pathway with or without an additional salE mutation confirmed that ethyl salicylate and salicylate were channeled into the β-ketoadipate pathway at the level of catechol and thence dissimilated by the cat gene products. SalR appeared to regulate expression of salA but not salE.

scholarly journals Suppression of a defect in the 5' untranslated leader of mitochondrial COX3 mRNA by a mutation affecting an mRNA-specific translational activator protein.

1993 ◽  
Vol 13 (8) ◽  
pp. 4806-4813 ◽  
Author(s):  
M C Costanzo ◽  
T D Fox
Keyword(s):  
Nuclear Gene ◽  
Gene Products ◽  
Wild Type ◽  
Large Deletions ◽  
Site Of Action ◽  
Genes Encoding ◽  
Cold Sensitive ◽  
Translational Activator ◽  
A Site ◽  
Dominant Suppressor

Translation of the Saccharomyces cerevisiae mitochondrial COX3 mRNA, encoding subunit III of cytochrome c oxidase, specifically requires the action of the nuclear gene products PET54, PET122, and PET494 at a site encoded in the 612-base 5' untranslated leader. To identify more precisely the site of action of the translational activators, we constructed two large deletions of the COX3 mRNA 5' untranslated leader. Both deletions blocked translation without affecting mRNA stability. However, one of the large deletions was able to revert to partial function by a small secondary deletion within the remaining 5' leader sequences. Translation of the resulting mutant (cox3-15) mRNA was still dependent on the nuclear-encoded specific activators but was cold sensitive. We selected revertants of this mitochondrial mutant at low temperature to identify genes encoding proteins that might interact with the COX3 mRNA 5' leader. One such revertant carried a missense mutation in the PET122 gene that was a strong and dominant suppressor of the cold-sensitive defect in the mRNA, indicating that the PET122 protein interacts functionally (possibly directly) with the COX3 mRNA 5' leader. The cox3-15 mutation was not suppressed by overproduction of the wild-type PET122 protein but was very weakly suppressed by overproduction of PET494 and slightly better suppressed by co-overproduction of PET494 and PET122.

scholarly journals The chromatin structure at the promoter of a glyceraldehyde phosphate dehydrogenase gene from Saccharomyces cerevisiae reflects its functional state.

1988 ◽  
Vol 8 (12) ◽  
pp. 5513-5520 ◽  
Author(s):  
B Pavlović ◽  
W Hörz
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromatin Structure ◽  
Carbon Sources ◽  
Initiation Site ◽  
Wild Type ◽  
Cis Acting ◽  
Genes Encoding ◽  
Nuclease Digestion ◽  
Dna Elements ◽  
Regulatory Dna

The chromatin structure of TDH3, one of three genes encoding glyceraldehyde phosphate dehydrogenases in Saccharomyces cerevisiae, was analyzed by nuclease digestion. A large hypersensitive region was found at the TDH3 promoter extending from the RNA initiation site at position -40 to position -560. This hypersensitive domain is nucleosome free and includes all putative cis-acting regulatory DNA elements. It is equally present in cells grown on fermentable as well as nonfermentable carbon sources. In a mutant which lacks the trans-activating protein GCR1 and which as a consequence expresses TDH3 at less than 5% of the wild-type level, the chromatin structure is different. Hypersensitivity between -40 and -370 is lost, due to the deposition of nucleosomes on a stretch that is nucleosome free in wild-type cells. Hypersensitivity is retained, however, further upstream (from -370 to -560). A similarly altered chromatin structure, as in a ger1 mutant, is found in wild-type cells when they approach stationary phase. This is the first evidence for a growth-dependent regulation of the TDH3 promoter.

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