scholarly journals Functional characterization of diverse ring-hydroxylating oxygenases and induction of complex aromatic catabolic gene clusters inSphingobiumsp. PNB

FEBS Open Bio ◽  
2014 ◽  
Vol 4 (1) ◽  
pp. 290-300 ◽  
Author(s):  
Pratick Khara ◽  
Madhumita Roy ◽  
Joydeep Chakraborty ◽  
Debajyoti Ghosal ◽  
Tapan K. Dutta
Keyword(s):  
Functional Characterization ◽  
Gene Clusters ◽  
Catabolic Gene

scholarly journals Plant Metabolic Gene Clusters: Evolution, Organization, and Their Applications in Synthetic Biology

2021 ◽  
Vol 12 ◽  
Author(s):  
Revuru Bharadwaj ◽  
Sarma R. Kumar ◽  
Ashutosh Sharma ◽  
Ramalingam Sathishkumar
Keyword(s):  
Synthetic Biology ◽  
Functional Characterization ◽  
Gene Clusters ◽  
Gene Clustering ◽  
Specific Gene ◽  
Gene Duplications ◽  
Ecological Functions ◽  
Specialized Metabolites ◽  
Coordinated Expression

Plants are a remarkable source of high-value specialized metabolites having significant physiological and ecological functions. Genes responsible for synthesizing specialized metabolites are often clustered together for a coordinated expression, which is commonly observed in bacteria and filamentous fungi. Similar to prokaryotic gene clustering, plants do have gene clusters encoding enzymes involved in the biosynthesis of specialized metabolites. More than 20 gene clusters involved in the biosynthesis of diverse metabolites have been identified across the plant kingdom. Recent studies demonstrate that gene clusters are evolved through gene duplications and neofunctionalization of primary metabolic pathway genes. Often, these clusters are tightly regulated at nucleosome level. The prevalence of gene clusters related to specialized metabolites offers an attractive possibility of an untapped source of highly useful biomolecules. Accordingly, the identification and functional characterization of novel biosynthetic pathways in plants need to be worked out. In this review, we summarize insights into the evolution of gene clusters and discuss the organization and importance of specific gene clusters in the biosynthesis of specialized metabolites. Regulatory mechanisms which operate in some of the important gene clusters have also been briefly described. Finally, we highlight the importance of gene clusters to develop future metabolic engineering or synthetic biology strategies for the heterologous production of novel metabolites.

scholarly journals Functional Characterization of Two Clusters of Brachypodium distachyon UDP-Glycosyltransferases Encoding Putative Deoxynivalenol Detoxification Genes

2013 ◽  
Vol 26 (7) ◽  
pp. 781-792 ◽  
Author(s):  
Wolfgang Schweiger ◽  
Jean-Claude Pasquet ◽  
Thomas Nussbaumer ◽  
Maria Paula Kovalsky Paris ◽  
Gerlinde Wiesenberger ◽  
...  
Keyword(s):  
Brachypodium Distachyon ◽  
Functional Characterization ◽  
Rapid Evolution ◽  
Gene Clusters ◽  
Single Copy ◽  
Wild Type ◽  
Vast Number ◽  
Putative Orthologs ◽  
Endogenous Substances

Plant small-molecule UDP-glycosyltransferases (UGT) glycosylate a vast number of endogenous substances but also act in detoxification of metabolites produced by plant-pathogenic microorganisms. The ability to inactivate the Fusarium graminearum mycotoxin deoxynivalenol (DON) into DON-3-O-glucoside is crucial for resistance of cereals. We analyzed the UGT gene family of the monocot model species Brachypodium distachyon and functionally characterized two gene clusters containing putative orthologs of previously identified DON-detoxification genes from Arabidopsis thaliana and barley. Analysis of transcription showed that UGT encoded in both clusters are highly inducible by DON and expressed at much higher levels upon infection with a wild-type DON-producing F. graminearum strain compared with infection with a mutant deficient in DON production. Expression of these genes in a toxin-sensitive strain of Saccharomyces cerevisiae revealed that only two B. distachyon UGT encoded by members of a cluster of six genes homologous to the DON-inactivating barley HvUGT13248 were able to convert DON into DON-3-O-glucoside. Also, a single copy gene from Sorghum bicolor orthologous to this cluster and one of three putative orthologs of rice exhibit this ability. Seemingly, the UGT genes undergo rapid evolution and changes in copy number, making it difficult to identify orthologs with conserved substrate specificity.

scholarly journals TworsaMhomologues encode central regulatory elements modulating quorum sensing expression inBurkholderia thailandensis

2017 ◽  
Author(s):  
Servane Le Guillouzer ◽  
Marie-Christine Groleau ◽  
Eric Déziel
Keyword(s):  
Quorum Sensing ◽  
Functional Characterization ◽  
Gene Clusters ◽  
Homoserine Lactone ◽  
Regulatory Elements ◽  
Burkholderia Thailandensis ◽  
Gene Coding ◽  
Genes Expression ◽  
In The Wild

AbstractThe bacteriumBurkholderia thailandensispossesses three conservedN-acyl-L-homoserine lactone (AHL) quorum sensing (QS) systems designated BtaI1/BtaR1 (QS-1), BtaI2/BtaR2 (QS-2), and BtaI3/BtaR3 (QS-3). These QS-systems are associated with the biosynthesis ofN-octanoyl-homoserine lactone (C8-HSL),N-3-hydroxy-decanoyl-homoserine lactone (3OHC10-HSL), as well asN-3-hydroxy-octanoyl-homoserine lactone (3OHC8-HSL), which are produced by the LuxI-type synthase BtaI1, BtaI2, and BtaI3, and modulated by the LuxR-type transcriptional regulators BtaR1, BtaR2, and BtaR3. BothbtaR1/btaI1andbtaR2/btaI2gene clusters contain an additional gene that is conserved in theBurkholderiagenus, homologous to a gene coding for the negative AHL biosynthesis modulatory protein RsaM originally identified in the phytopathogenPseudomonas fuscovaginae, and hence designatedrsaM1andrsaM2. We have characterized the function of these tworsaMhomologues and demonstrated their involvement in the regulation of AHLs biosynthesis inB. thailandensisstrain E264. We measured the production of C8-HSL, 3OHC10-HSL, and 3OHC8-HSL by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) in the wild-type strain and in thersaM1-andrsaM2-mutants, and monitored the transcription ofbtaI1,btaI2, andbtaI3 using chromosomal mini-CTX-luxtranscriptional reporters. The expression ofbtaR1,btaR2, andbtaR3 was also measured by quantitative everse-transcription PCR (qRT-PCR). We demonstrate that the QS-1 system is repressed by RsaM1, whereas RsaM2 principally represses the QS-2 system. We also found that bothrsaM1andrsaM2are QS-controlled, as well as negatively auto-regulated. We conclude that RsaM1 and RsaM2 are an integral part of the QS modulatory circuitry ofB. thailandensis, and play a major role in the hierarchical and homeostatic organization of the QS-1, QS-2, and QS-3 systems.ImportanceQuorum sensing (QS) is a global regulatory mechanism of genes expression depending on bacterial density. QS is commonly involved in the coordination of genes expression associated with the establishment of host-pathogen interactions and acclimatization to the environment. We present the functional characterization of the tworsaMhomologues designatedrsaM1andrsaM2in the regulation of the multiple QS systems coexisting in the non-pathogenic bacteriumBurkholderia thailandensis, widely used as a model system for the study of the pathogenBurkholderia pseudomallei. We found that inactivation of thesersaMhomologues, which are clustered with the other QS genes, profoundly affects the QS regulatory circuity ofB. thailandensis. It is proposed that these genes code for QS repressors and we conclude that they constitute essential regulatory components of the QS modulatory network ofB. thailandensis, and provide additional layers of regulation to modulate the expression of QS-controlled genes, including those encoding virulence/survival factors and linked to environmental adaptation inB. pseudomallei.

scholarly journals The Chemical Structure of Widespread Microbial Aryl Polyene Lipids

2020 ◽  
Author(s):  
Gina L. C. Grammbitter ◽  
Yi-Ming Shi ◽  
Yan-Ni Shi ◽  
Sahithya P. B. Vemulapalli ◽  
Christian Richter ◽  
...  
Keyword(s):  
Isotope Labeling ◽  
Functional Characterization ◽  
Gene Clusters ◽  
Fatty Acyl ◽  
Ecological Niches ◽  
Biosynthetic Gene Clusters ◽  
Chromatographic Separations ◽  
Protective Function ◽  
Natural Function

AbstractBiosynthetic gene clusters (BGC) involved in aryl polyene (APE) biosynthesis are supposed to represent the most widespread BGC in the bacterial world.[1–3] Still, only hydrolysis products[4–8] and not the full-length product(s) have been identified, hindering studies on their biosynthesis and natural function. Here, we apply subsequent chromatographic separations to purify the aryl polyene-containing lipids (APELs) from the entomopathogenic bacterium Xenorhabdus doucetiae. Structure elucidation using a combination of isotope labeling, nuclear magnetic resonance techniques, and tandem mass spectrometry reveals an array of APELs featuring an all-trans C26:5 conjugated fatty acyl and a galactosamine-phosphate-glycerol moiety. In combination with extensive genetic studies, this research broadens the bacterial natural product repertoire and paves the way for future functional characterization of this almost universal microbial compound class. Due to their protective function against reactive oxygen species,[5,9] APELs might be important for virulence or symbiosis, mediating organismic interactions in several ecological niches.

scholarly journals Functional Characterization of a Composite Bacteriocin Locus from Malt Isolate Lactobacillus sakei 5

2003 ◽  
Vol 69 (12) ◽  
pp. 7194-7203 ◽  
Author(s):  
Anne Vaughan ◽  
Vincent G. H. Eijsink ◽  
Douwe van Sinderen
Keyword(s):  
Gene Cluster ◽  
Functional Characterization ◽  
Gene Clusters ◽  
Comparative Sequence Analysis ◽  
Accessory Protein ◽  
Lactobacillus Sakei ◽  
Structural Genes ◽  
Immunity Genes ◽  
Class Iib

ABSTRACT Lactobacillus sakei 5, isolated from malted barley, produces three bacteriocins. Genetic and functional analysis of the purified bacteriocins showed that this strain produces a plasmid-encoded bacteriocin that is identical to sakacin P, as well as two novel, chromosomally encoded bacteriocins, which were designated sakacin T and sakacin X. The structural genes specifying sakacin T and sakacin X are part of the sakacin TX locus, which consists of two adjacent but divergently oriented gene clusters. The first gene cluster includes stxP, stxR, stxK, and stxT, which, based on functional and comparative sequence analysis, are believed to encode an inducing peptide and proteins involved in regulation and secretion of these bacteriocins. The second gene cluster includes the structural and immunity genes for sakacin T, a class IIb two-peptide bacteriocin composed of SakTα and SakTβ, and sakacin X, a class IIa bacteriocin. Interestingly, a so-called transport accessory protein was absent from the locus, and based on our results it appears that a dedicated accessory protein is not required for processing and transport of sakacin T and sakacin X.

Functional characterization of human brown adipose tissue metabolism

2020 ◽  
Vol 477 (7) ◽  
pp. 1261-1286 ◽  
Author(s):  
Marie Anne Richard ◽  
Hannah Pallubinsky ◽  
Denis P. Blondin
Keyword(s):  
Adipose Tissue ◽  
Brown Adipose Tissue ◽  
Functional Characterization ◽  
Human Infants ◽  
Positron Emission ◽  
Brown Adipose ◽  
Treatment Of Obesity ◽  
And Function

Brown adipose tissue (BAT) has long been described according to its histological features as a multilocular, lipid-containing tissue, light brown in color, that is also responsive to the cold and found especially in hibernating mammals and human infants. Its presence in both hibernators and human infants, combined with its function as a heat-generating organ, raised many questions about its role in humans. Early characterizations of the tissue in humans focused on its progressive atrophy with age and its apparent importance for cold-exposed workers. However, the use of positron emission tomography (PET) with the glucose tracer [18F]fluorodeoxyglucose ([18F]FDG) made it possible to begin characterizing the possible function of BAT in adult humans, and whether it could play a role in the prevention or treatment of obesity and type 2 diabetes (T2D). This review focuses on the in vivo functional characterization of human BAT, the methodological approaches applied to examine these features and addresses critical gaps that remain in moving the field forward. Specifically, we describe the anatomical and biomolecular features of human BAT, the modalities and applications of non-invasive tools such as PET and magnetic resonance imaging coupled with spectroscopy (MRI/MRS) to study BAT morphology and function in vivo, and finally describe the functional characteristics of human BAT that have only been possible through the development and application of such tools.

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