scholarly journals Organization and Regulation of Pentachlorophenol-Degrading Genes in Sphingobium chlorophenolicum ATCC 39723

2002 ◽  
Vol 184 (17) ◽  
pp. 4672-4680 ◽  
Author(s):  
Mian Cai ◽  
Luying Xun
Keyword(s):  
Transcriptional Regulator ◽  
Degradation Pathway ◽  
Gene Products ◽  
Regulator Gene ◽  
New Genes ◽  
Reductase Gene ◽  
Sphingomonas Chlorophenolica ◽  
Sphingobium Chlorophenolicum ◽  
Maleylacetate Reductase ◽  
Regulator Genes

ABSTRACT The first three enzymes of the pentachlorophenol (PCP) degradation pathway in Sphingobium chlorophenolicum (formerly Sphingomonas chlorophenolica) ATCC 39723 have been characterized, and the corresponding genes, pcpA, pcpB, and pcpC, have been individually cloned and sequenced. To search for new genes involved in PCP degradation and map the physical locations of the pcp genes, a 24-kb fragment containing pcpA and pcpC was completely sequenced. A putative LysR-type transcriptional regulator gene, pcpM, and a maleylacetate reductase gene, pcpE, were identified upstream of pcpA. pcpE was found to play a role in PCP degradation. pcpB was not found on the 24-kb fragment. The four gene products PcpB, PcpC, PcpA, and PcpE were responsible for the metabolism of PCP to 3-oxoadipate in ATCC 39723, and inactivational mutation of each gene disrupted the degradation pathway. The organization of the pcp genes is unusual because the four PCP-degrading genes, pcpA, pcpB, pcpC, and pcpE, were found to be located at four discrete locations. Two hypothetical LysR-type regulator genes, pcpM and pcpR, have been identified; pcpM was not required, but pcpR was essential for the induction of pcpB, pcpA, and pcpE. The coinducers of PcpR were PCP and other polychlorinated phenols. The expression of pcpC was constitutive. Thus, the organization and regulation of the genes involved in PCP degradation to 3-oxoadipate were documented.

PCR detection of pathogenic Leptospira genomospecies targeting putative transcriptional regulator genes

2006 ◽  
Vol 52 (3) ◽  
pp. 272-277 ◽  
Author(s):  
Dongyou Liu ◽  
Mark L Lawrence ◽  
Frank W Austin ◽  
A Jerald Ainsworth ◽  
Lanny W Pace
Keyword(s):  
Molecular Mechanisms ◽  
Control Strategies ◽  
Transcriptional Regulator ◽  
Diagnostic Procedures ◽  
Pcr Primers ◽  
Regulator Gene ◽  
Pathogenic Leptospira ◽  
Pathogenic Potential ◽  
Diagnostic Potential ◽  
Regulator Genes

The genus Leptospira comprises multiple genomospecies that demonstrate varied pathogenic potential. The availability of rapid and precise diagnostic procedures to differentiate pathogenic from nonpathogenic Leptospira spp. is therefore essential to prevent an otherwise easily treatable malaise from developing into a life-threatening disease. In this report, we conducted an investigation on the diagnostic potential of Leptospira genes encoding putative tran scriptional regulators. While PCR primers derived from transcriptional regulator gene la1137 recognized all 24 pathogenic Leptospira strains representing seven species, those from la1937, la3231, la3825, and la4130 detected 19 of the 24 Leptospira strains. However, none of these primers reacted with four nonpathogenic Leptospira species or other common bacteria. The putative transcriptional regulator genes la1137, la1937, la3231, la3825, and la4130 are present in pathogenic Leptospira strains, making them potential targets for diagnostic applications. Further characterization of these genes and their proteins may help elucidate the molecular mechanisms of leptospiral virulence and pathogenicity and pave the way for potential development of novel control strategies against leptospirosis.Key words: Leptospira, pathogenic, transcriptional regulator gene, PCR, identification.

scholarly journals Insights into functional and evolutionary analysis of carbaryl metabolic pathway from Pseudomonas sp. strain C5pp

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Vikas D. Trivedi ◽  
Pramod Kumar Jangir ◽  
Rakesh Sharma ◽  
Prashant S. Phale
Keyword(s):  
Draft Genome ◽  
Degradation Pathway ◽  
Evolutionary Analysis ◽  
Extradiol Dioxygenase ◽  
Transfer Event ◽  
New Family ◽  
New Genes ◽  
Catabolic Genes ◽  
Soil Isolate ◽  
Genes Encoding

Abstract Carbaryl (1-naphthyl N-methylcarbamate) is a most widely used carbamate pesticide in the agriculture field. Soil isolate, Pseudomonas sp. strain C5pp mineralizes carbaryl via 1-naphthol, salicylate and gentisate, however the genetic organization and evolutionary events of acquisition and assembly of pathway have not yet been studied. The draft genome analysis of strain C5pp reveals that the carbaryl catabolic genes are organized into three putative operons, ‘upper’, ‘middle’ and ‘lower’. The sequence and functional analysis led to identification of new genes encoding: i) hitherto unidentified 1-naphthol 2-hydroxylase, sharing a common ancestry with 2,4-dichlorophenol monooxygenase; ii) carbaryl hydrolase, a member of a new family of esterase; and iii) 1,2-dihydroxy naphthalene dioxygenase, uncharacterized type-II extradiol dioxygenase. The ‘upper’ pathway genes were present as a part of a integron while the ‘middle’ and ‘lower’ pathway genes were present as two distinct class-I composite transposons. These findings suggest the role of horizontal gene transfer event(s) in the acquisition and evolution of the carbaryl degradation pathway in strain C5pp. The study presents an example of assembly of degradation pathway for carbaryl.

scholarly journals Maintenance Role of a Glutathionyl-Hydroquinone Lyase (PcpF) in Pentachlorophenol Degradation by Sphingobium chlorophenolicum ATCC 39723

2008 ◽  
Vol 190 (23) ◽  
pp. 7595-7600 ◽  
Author(s):  
Yan Huang ◽  
Randy Xun ◽  
Guanjun Chen ◽  
Luying Xun
Keyword(s):  
Degradation Rate ◽  
Tricarboxylic Acid Cycle ◽  
Degradation Pathway ◽  
Tricarboxylic Acid ◽  
Metabolic Intermediate ◽  
Reductive Dehalogenase ◽  
Cell Extracts ◽  
Toxic Pollutant ◽  
Sphingobium Chlorophenolicum

ABSTRACT Pentachlorophenol (PCP) is a toxic pollutant. Its biodegradation has been extensively studied in Sphingobium chlorophenolicum ATCC 39723. All enzymes required to convert PCP to a common metabolic intermediate before entering the tricarboxylic acid cycle have been characterized. One of the enzymes is tetrachloro-p-hydroquinone (TeCH) reductive dehalogenase (PcpC), which is a glutathione (GSH) S-transferase (GST). PcpC catalyzes the GSH-dependent conversion of TeCH to trichloro-p-hydroquinone (TriCH) and then to dichloro-p-hydroquinone (DiCH) in the PCP degradation pathway. PcpC is susceptible to oxidative damage, and the damaged PcpC produces glutathionyl (GS) conjugates, GS-TriCH and GS-DiCH, which cannot be further metabolized by PcpC. The fate and effect of GS-hydroquinone conjugates were unknown. A putative GST gene (pcpF) is located next to pcpC on the bacterial chromosome. The pcpF gene was cloned, and the recombinant PcpF was purified. The purified PcpF was able to convert GS-TriCH and GS-DiCH conjugates to TriCH and DiCH, respectively. The GS-hydroquinone lyase reactions catalyzed by PcpF are rather unusual for a GST. The disruption of pcpF in S. chlorophenolicum made the mutant lose the GS-hydroquinone lyase activities in the cell extracts. The mutant became more sensitive to PCP toxicity and had a significantly decreased PCP degradation rate, likely due to the accumulation of the GS-hydroquinone conjugates inside the cell. Thus, PcpF played a maintenance role in PCP degradation and converted the GS-hydroquinone conjugates back to the intermediates of the PCP degradation pathway.

scholarly journals Autophagy gene-dependent intracellular immunity triggered by interferon-γ

2021 ◽  
Author(s):  
Michael R McAllaster ◽  
Jaya Bhushan ◽  
Dale R Balce ◽  
Anthony Orvedahl ◽  
Arnold Park ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Interferon Γ ◽  
Degradation Pathway ◽  
Lysosomal Degradation ◽  
Cellular Processes ◽  
Binding Domains ◽  
New Genes ◽  
Autophagy Gene ◽  
Atg Genes ◽  
Dependent Processes

Genes required for the lysosomal degradation pathway of autophagy play key roles in topologically distinct cellular processes with significant physiologic importance. One of the first-described of these ATG gene-dependent processes is the requirement for a subset of ATG genes in interferon-γ (IFNγ)-induced inhibition of Norovirus and Toxoplasma gondii replication. Herein we identified new genes that are required for or that negatively regulate this immune mechanism. Enzymes involved in the conjugation of UFM1 to target proteins including UFC1 and UBA5, negatively regulated IFNγ-induced inhibition of norovirus replication via effects of Ern1. IFNγ-induced inhibition of norovirus replication required Wipi2b and Atg9a, but not Becn1 (encoding Beclin1), Atg14, or Sqstm1. The phosphatidylinositol-3-phosphate and ATG16L1 binding domains of WIPI2B were required for IFNγ-induced inhibition of norovirus replication. Both WIPI2 and SQSTM1 were required for IFN?-induced inhibition of Toxoplasma gondii replication in HeLa cells. These studies further delineate the mechanisms of a programmable form of cytokine-induced intracellular immunity that relies on an expanding cassette of essential ATG genes to restrict the growth of phylogenetically diverse pathogens.

Transcriptional regulation of cytoskeletal functions and segmentation by a novel maternal pair-rule gene, lilliputian

Development ◽  
2001 ◽  
Vol 128 (5) ◽  
pp. 801-813 ◽  
Author(s):  
A.H. Tang ◽  
T.P. Neufeld ◽  
G.M. Rubin ◽  
H.A. Muller
Keyword(s):  
Transcriptional Control ◽  
Fragile X ◽  
Transcriptional Regulator ◽  
Regulator Gene ◽  
Embryonic Patterning ◽  
Fushi Tarazu ◽  
Fragile X Mental Retardation ◽  
Pair Rule Gene ◽  
Mutant Phenotypes ◽  
Pair Rule

Transcriptional control during early Drosophila development is governed by maternal and zygotic factors. We have identified a novel maternal transcriptional regulator gene, lilliputian (lilli), which contains an HMG1 (AT-hook) motif and a domain with similarity to the human fragile X mental retardation FMR2 protein and the AF4 proto-oncoprotein. Embryos lacking maternal lilli expression show specific defects in the establishment of a functional cytoskeleton during cellularization, and exhibit a pair-rule segmentation phenotype. These mutant phenotypes correlate with markedly reduced expression of the early zygotic genes serendipity alpha, fushi tarazu and huckebein, which are essential for cellularization and embryonic patterning. In addition, loss of lilli in adult photoreceptor and bristle cells results in a significant decrease in cell size. Our results indicate that lilli represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis.

scholarly journals Hypothesis: protein and RNA attributes are continuously optimized over time

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Sidney B. Cambridge
Keyword(s):  
Protein Structure ◽  
Gene Function ◽  
Protein Abundance ◽  
Gene Products ◽  
Gene Conservation ◽  
New Genes ◽  
Temporal Path ◽  
Gene Age ◽  
Over Time

Abstract Background Little is known why proteins and RNAs exhibit half-lives varying over several magnitudes. Despite many efforts, a conclusive link between half-lives and gene function could not be established suggesting that other determinants may influence these molecular attributes. Results Here, I find that with increasing gene age there is a gradual and significant increase of protein and RNA half-lives, protein structure, and other molecular attributes that tend to affect protein abundance. These observations are accommodated in a hypothesis which posits that new genes at ‘birth’ are not optimized and thus their products exhibit low half-lives and less structure but continuous mutagenesis eventually improves these attributes. Thus, the protein and RNA products of the oldest genes obtained their high degrees of stability and structure only after billions of years while the products of younger genes had less time to be optimized and are therefore less stable and structured. Because more stable proteins with lower turnover require less transcription to maintain the same level of abundance, reduced transcription-associated mutagenesis (TAM) would fixate the changes by increasing gene conservation. Conclusions Consequently, the currently observed diversity of molecular attributes is a snapshot of gene products being at different stages along their temporal path of optimization.

Characterization of the Maleylacetate Reductase MacA of Rhodococcus opacus 1CP and Evidence for the Presence of an Isofunctional Enzyme

1998 ◽  
Vol 180 (14) ◽  
pp. 3503-3508 ◽  
Author(s):  
Volker Seibert ◽  
Elena M. Kourbatova ◽  
Ludmila A. Golovleva ◽  
Michael Schlömann
Keyword(s):  
Aromatic Compounds ◽  
Gene Clusters ◽  
Reductive Dehalogenation ◽  
Rhodococcus Opacus ◽  
Reductase Gene ◽  
Rhodococcus Opacus 1Cp ◽  
Dienelactone Hydrolase ◽  
Maleylacetate Reductase ◽  
Intradiol Dioxygenase

ABSTRACT Maleylacetate reductases (EC 1.3.1.32 ) have been shown to contribute not only to the bacterial catabolism of some usual aromatic compounds like quinol or resorcinol but also to the degradation of aromatic compounds carrying unusual substituents, such as halogen atoms or nitro groups. Genes coding for maleylacetate reductases so far have been analyzed mainly in chloroaromatic compound-utilizing proteobacteria, in which they were found to belong to specialized gene clusters for the turnover of chlorocatechols or 5-chlorohydroxyquinol. We have now cloned the gene macA, which codes for one of apparently (at least) two maleylacetate reductases in the gram-positive, chlorophenol-degrading strain Rhodococcus opacus 1CP. Sequencing of macA showed the gene product to be relatively distantly related to its proteobacterial counterparts (ca. 42 to 44% identical positions). Nevertheless, like the known enzymes from proteobacteria, the cloned Rhodococcusmaleylacetate reductase was able to convert 2-chloromaleylacetate, an intermediate in the degradation of dichloroaromatic compounds, relatively fast and with reductive dehalogenation to maleylacetate. Among the genes ca. 3 kb up- and downstream of macA, none was found to code for an intradiol dioxygenase, a cycloisomerase, or a dienelactone hydrolase. Instead, the only gene which is likely to be cotranscribed with macA encodes a protein of the short-chain dehydrogenase/reductase family. Thus, the R. opacus maleylacetate reductase genemacA clearly is not part of a specialized chlorocatechol gene cluster.

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