A survey of indigenous microbial hydrocarbon degradation genes in soils from Antarctica and Brazil

2004 ◽  
Vol 50 (5) ◽  
pp. 323-333 ◽  
Author(s):  
A P Luz ◽  
V H Pellizari ◽  
L G Whyte ◽  
C W Greer
Keyword(s):  
Petroleum Hydrocarbons ◽  
Hybridization Analysis ◽  
Soil Extracts ◽  
Antarctic Soils ◽  
Catabolic Genes ◽  
Genes Encoding ◽  
Total Community ◽  
Alkane Monooxygenase ◽  
And Control ◽  
Total Community Dna

Total community DNA from 29 noncontaminated soils and soils impacted by petroleum hydrocarbons and chloro-organics from Antarctica and Brazil were screened for the presence of nine catabolic genes, encoding alkane monooxygenase or aromatic dioxygenases, from known bacterial biodegradation pathways. Specific primers and probes targeting alkane monooxygenase genes were derived from Pseudomonas putida ATCC 29347 (Pp alkB), Rhodococcus sp. strain Q15 (Rh alkB1, Rh alkB2), and Acinetobacter sp. ADP-1 (Ac alkM). In addition, primers and probes detecting aromatic dioxygenase genes were derived from P. putida ATCC 17484 (ndoB), P. putida F1 (todC1), P. putida ATCC 33015 (xylE and cat23), and P. pseudoalcaligenes KF707 (bphA). The primers and probes were used to analyze total community DNA extracts by using PCR and hybridization analysis. All the catabolic genes, except the Ac alkM, were detected in contaminated and control soils from both geographic regions, with a higher frequency in the Antarctic soils. The alkane monooxygenase genes, Rh alkB1 and Rh alkB2, were the most frequently detected alk genes in both regions, while Pp alkB was not detected in Brazil soils. Genes encoding the aromatic dioxygenases toluene dioxygenase (todC1) and biphenyl dioxygenase (bphA) were the most frequently detected in Antarctica, and todC1 and catechol-2,3-dioxygenase (cat23) were the most frequent in Brazil soils. Hybridization analysis confirmed the PCR results, indicating that the probes used had a high degree of homology to the genes detected in the soil extracts and were effective in detecting biodegradative potential in the indigenous microbial population.Key words: catabolic genes, anthropogenic compounds, petroleum hydrocarbons, alkane monooxygenases, aromatic dioxygenases.

scholarly journals 40S ribosome profiling reveals distinct roles for Tma20/Tma22 (MCT-1/DENR) and Tma64 (eIF2D) in 40S subunit recycling

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
David J. Young ◽  
Sezen Meydan ◽  
Nicholas R. Guydosh
Keyword(s):  
Protein Synthesis ◽  
Neurological Disease ◽  
Ribosome Profiling ◽  
Minor Role ◽  
Stop Codons ◽  
Genes Encoding ◽  
Ribosome Footprinting ◽  
A Minor ◽  
And Control ◽  
In Cells

AbstractThe recycling of ribosomes at stop codons for use in further rounds of translation is critical for efficient protein synthesis. Removal of the 60S subunit is catalyzed by the ATPase Rli1 (ABCE1) while removal of the 40S is thought to require Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR). However, it remains unclear how these Tma proteins cause 40S removal and control reinitiation of downstream translation. Here we used a 40S ribosome footprinting strategy to directly observe intermediate steps of ribosome recycling in cells. Deletion of the genes encoding these Tma proteins resulted in broad accumulation of unrecycled 40S subunits at stop codons, directly establishing their role in 40S recycling. Furthermore, the Tma20/Tma22 heterodimer was responsible for a majority of 40S recycling events while Tma64 played a minor role. Introduction of an autism-associated mutation into TMA22 resulted in a loss of 40S recycling activity, linking ribosome recycling and neurological disease.

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 WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 719 ◽  
Author(s):  
Mingdong Zhu ◽  
Hongjun Xie ◽  
Xiangjin Wei ◽  
Komivi Dossa ◽  
Yaying Yu ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Biological Processes ◽  
Salt Tolerant ◽  
Hub Genes ◽  
Pathway Gene ◽  
Salt Response ◽  
Genes Encoding ◽  
Bioinformatic Approaches ◽  
Salt Tolerant Cultivars ◽  
And Control

Rice, being a major staple food crop and sensitive to salinity conditions, bears heavy yield losses due to saline soil. Although some salt responsive genes have been identified in rice, their applications in developing salt tolerant cultivars have resulted in limited achievements. Herein, we used bioinformatic approaches to perform a meta-analysis of three transcriptome datasets from salinity and control conditions in order to reveal novel genes and the molecular pathways underlying rice response to salt. From a total of 28,432 expressed genes, we identify 457 core differentially expressed genes (DEGs) constitutively responding to salt, regardless of the stress duration, genotype, or the tissue. Gene co-expression analysis divided the core DEGs into three different modules, each of them contributing to salt response in a unique metabolic pathway. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses highlighted key biological processes and metabolic pathways involved in the salt response. We identified important novel hub genes encoding proteins of different families including CAM, DUF630/632, DUF581, CHL27, PP2-13, LEA4-5, and transcription factors, which could be functionally characterized using reverse genetic experiments. This novel repertoire of candidate genes related to salt response in rice will be useful for engineering salt tolerant varieties.

scholarly journals Priming of Defense Systems and Upregulation of MYC2 and JAZ1 Genes after Botrytis cinerea Inoculation in Methyl Jasmonate-Treated Strawberry Fruits

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 447 ◽  
Author(s):  
Felipe Valenzuela-Riffo ◽  
Paz E. Zúñiga ◽  
Luis Morales-Quintana ◽  
Mauricio Lolas ◽  
Marcela Cáceres ◽  
...  
Keyword(s):  
Methyl Jasmonate ◽  
Botrytis Cinerea ◽  
Defense Responses ◽  
Gray Mold ◽  
The Past ◽  
Defense Systems ◽  
Meja Treatment ◽  
Fruit Development And Ripening ◽  
Genes Encoding ◽  
And Control

Several attempts have been made to study the effects of methyl jasmonate (MeJA) on plants in the past years. However, the comparative effects of the number and phenological time of MeJA applications on the activation of defense systems is currently unknown in strawberries. In the present research, we performed three field treatments during strawberry (Fragaria × ananassa ‘Camarosa’) fruit development and ripening which consisted of differential MeJA applications at flowering (M3), and the large green (M2 and M3) and red ripe (M1, M2, and M3) fruit stages. We also checked changes in gene expression related to plant defense against Botrytis cinerea inoculation post-harvest. In M3 treatment, we observed an upregulation of the anthocyanin and lignin contents and the defense-related genes, encoding for chitinases, β-1,3-glucanases and polygalacturonase-inhibiting proteins, after harvest (0 hpi), along with the jasmonate signaling-related genes FaMYC2 and FaJAZ1 at 48 h after B. cinerea inoculation (48 hpi) during postharvest storage. Although we did not find differences in gray mold incidence between the MeJA treatments and control, these results suggest that preharvest MeJA treatment from the flowering stage onwards (M3) primes defense responses mediated by the upregulation of different defense-related genes and retains the upregulation of MYC2 and JAZ1 at 48 hpi.

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.

Differentiation of Schistosoma mansoni from S. rodhaini using cloned DNA probes

Parasitology ◽  
1989 ◽  
Vol 98 (1) ◽  
pp. 75-80 ◽  
Author(s):  
Tina K. Walker ◽  
A. J. G. Simpson ◽  
D. Rollinson
Keyword(s):  
Schistosoma Mansoni ◽  
Blot Hybridization ◽  
Repeated Sequence ◽  
Transcription Unit ◽  
Hybridization Analysis ◽  
Rrna Gene ◽  
Dot Blot ◽  
Restriction Sites ◽  
Genes Encoding ◽  
Female Specific

SummaryThe ribosomal RNA (rRNA) gene units of Schistosoma mansoni and S. rodhaini, of the lateral spined egg group, have been studied. The schistosome rRNA gene unit consists of a regular interspersion of the two genes encoding the large and small rRNA units with two spacers. The large spacer is not transcribed while the small spacer is part of the transcription unit. Variation in the rRNA gene unit between the two species is demonstrated to take the form of loss or gain of restriction sites within the non-transcribed and transcribed spacers. This variation has been demonstrated to enable the differentiation of S. mansoni from S. rodhaini by Southern hybridization analysis. In addition, a DNA clone representing a female specific, tandemly repeated sequence, is demonstrated to enable differentiation of S. mansoni and S. rodhaini using dot blot hybridization analysis.

scholarly journals Skeletal muscle gene expression after myostatin knockout in mature mice

2009 ◽  
Vol 38 (3) ◽  
pp. 342-350 ◽  
Author(s):  
Stephen Welle ◽  
Andrew Cardillo ◽  
Michelle Zanche ◽  
Rabi Tawil
Keyword(s):  
Gene Expression ◽  
Muscle Development ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Muscle Gene Expression ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Muscle Gene ◽  
Or Genes ◽  
And Control

There is much interest in developing anti-myostatin agents to reverse or prevent muscle atrophy in adults, so it is important to characterize the effects of reducing myostatin activity after normal muscle development. For assessment of the effect of loss of myostatin signaling on gene expression in muscle, RNA from mice with postdevelopmental myostatin knockout was analyzed with oligonucleotide microarrays. Myostatin was undetectable in muscle within 2 wk after Cre recombinase activation in 4-month-old male mice with floxed myostatin genes. Three months after myostatin depletion, muscle mass had increased 26% (vs. 2% after induction of Cre activity in mice with normal myostatin genes), at which time the expression of several hundred genes differed in knockout and control mice at nominal P < 0.01. In contrast to previously reported effects of constitutive myostatin knockout, postdevelopmental knockout did not downregulate expression of genes encoding slow isoforms of contractile proteins or genes encoding proteins involved in energy metabolism. Several collagen genes were expressed at 20–50% lower levels in the myostatin-deficient muscles, which had ∼25% less collagen than normal muscles as reflected by hydroxyproline content. Most of the other genes affected by myostatin depletion have not been previously linked to myostatin signaling. Gene set enrichment analysis suggested that Smads are not the only transcription factors with reduced activity after myostatin depletion. These data reinforce other evidence that myostatin regulates collagen production in muscle and demonstrate that many of the previously reported effects of constitutive myostatin deficiency do not occur when myostatin is knocked out in mature muscles.

scholarly journals Biodegradation of total petroleum hydrocarbons in contaminated soils using indigenous bacterial consortium

2020 ◽  
Vol 7 (2) ◽  
pp. 127-133
Author(s):  
Yalda Basim ◽  
Ghasemali Mohebali ◽  
Sahand Jorfi ◽  
Ramin Nabizadeh ◽  
Mehdi Ahmadi Moghadam ◽  
...  
Keyword(s):  
Contaminated Soils ◽  
Petroleum Hydrocarbons ◽  
Environmental Concern ◽  
Bacterial Consortium ◽  
Oil Field ◽  
Total Petroleum Hydrocarbons ◽  
Bacterial Strains ◽  
Flame Ionization ◽  
And Control ◽  
Similar Texture

Background: Biodegradation of hydrocarbon compounds is a great environmental concern due to their toxic nature and ubiquitous occurrence. In this study, biodegradation potential of oily soils was investigated in an oil field using indigenous bacterial consortium. Methods: The bacterial strains present in the contaminated and non-contaminated soils were identified via DNA extraction using 16S rDNA gene sequencing during six months. Furthermore, total petroleum hydrocarbons (TPH) were removed from oil-contaminated soils. The TPH values were determined using a gas chromatograph equipped with a flame ionization detector (GC-FID). Results: The bacterial consortium identified in oil-contaminated soils (case) belonged to the families Halomonadaceae (91.5%) and Bacillaceae (8.5%), which was significantly different from those identified in non-contaminated soils (control) belonging to the families Enterobacteriaceae (84.6%), Paenibacillaceae (6%), and Bacillaceae (9.4%). It was revealed that the diversity of bacterial strains was less in oil-contaminated soils and varied significantly between case and control samples. Indigenous bacterial consortium was used in oil-contaminated soils without need for amplification of heterogeneous bacteria and the results showed that the identified bacterial strains could be introduced as a sufficient consortium for biodegradation of oil-contaminated soils with similar texture, which is one of the innovative aspects of this research. Conclusion: An oil-contaminated soil sample with TPH concentration of 1640 mg/kg was subjected to bioremediation during 6 months using indigenous bacterial consortium and a TPH removal efficiency of 28.1% was obtained.

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