Chromosomal assignments for porcine genes encoding enzymes in hepatic metabolic pathways

2002 ◽  
Vol 33 (4) ◽  
pp. 255-263 ◽  
Author(s):  
K. Wimmers ◽  
S. Ponsuksili ◽  
U. Bläser ◽  
J. Gellin ◽  
K. Schellander
Keyword(s):  
Metabolic Pathways ◽  
Genes Encoding

scholarly journals A Transcriptomic Approach to the Metabolism of Tetrapyrrolic Photosensitizers in a Marine Annelid

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3924
Author(s):  
Maria Leonor Santos ◽  
Mariaelena D’Ambrosio ◽  
Ana P. Rodrigo ◽  
A. Jorge Parola ◽  
Pedro M. Costa
Keyword(s):  
Metabolic Pathways ◽  
Molecular Networks ◽  
Bile Pigments ◽  
Rna Seq ◽  
The Past ◽  
Wide Range ◽  
Genes Encoding ◽  
Organ Specific ◽  
Bright Green ◽  
Green Coloration

The past decade has seen growing interest in marine natural pigments for biotechnological applications. One of the most abundant classes of biological pigments is the tetrapyrroles, which are prized targets due their photodynamic properties; porphyrins are the best known examples of this group. Many animal porphyrinoids and other tetrapyrroles are produced through heme metabolic pathways, the best known of which are the bile pigments biliverdin and bilirubin. Eulalia is a marine Polychaeta characterized by its bright green coloration resulting from a remarkably wide range of greenish and yellowish tetrapyrroles, some of which have promising photodynamic properties. The present study combined metabolomics based on HPLC-DAD with RNA-seq transcriptomics to investigate the molecular pathways of porphyrinoid metabolism by comparing the worm’s proboscis and epidermis, which display distinct pigmentation patterns. The results showed that pigments are endogenous and seemingly heme-derived. The worm possesses homologs in both organs for genes encoding enzymes involved in heme metabolism such as ALAD, FECH, UROS, and PPOX. However, the findings also indicate that variants of the canonical enzymes of the heme biosynthesis pathway can be species- and organ-specific. These differences between molecular networks contribute to explain not only the differential pigmentation patterns between organs, but also the worm’s variety of novel endogenous tetrapyrrolic compounds.

scholarly journals Mutagenesis of the C1 Oxidation Pathway in Methanosarcina barkeri: New Insights into the Mtr/Mer Bypass Pathway

2008 ◽  
Vol 190 (6) ◽  
pp. 1928-1936 ◽  
Author(s):  
Paula V. Welander ◽  
William W. Metcalf
Keyword(s):  
Metabolic Pathways ◽  
Methanosarcina Barkeri ◽  
Growth Substrate ◽  
Oxidation Of Methanol ◽  
Cell Extracts ◽  
Oxidation Reduction ◽  
Absolute Requirement ◽  
Genes Encoding ◽  
Encoding Gene

ABSTRACT A series of Methanosarcina barkeri mutants lacking the genes encoding the enzymes involved in the C1 oxidation/reduction pathway were constructed. Mutants lacking the methyl-tetrahydromethanopterin (H4MPT):coenzyme M (CoM) methyltransferase-encoding operon (Δmtr), the methylene-H4MPT reductase-encoding gene (Δmer), the methylene-H4MPT dehydrogenase-encoding gene (Δmtd), and the formyl-methanofuran:H4MPT formyl-transferase-encoding gene (Δftr) all failed to grow using either methanol or H2/CO2 as a growth substrate, indicating that there is an absolute requirement for the C1 oxidation/reduction pathway for hydrogenotrophic and methylotrophic methanogenesis. The mutants also failed to grow on acetate, and we suggest that this was due to an inability to generate the reducing equivalents needed for biosynthetic reactions. Despite their lack of growth on methanol, the Δmtr and Δmer mutants were capable of producing methane from this substrate, whereas the Δmtd and Δftr mutants were not. Thus, there is an Mtr/Mer bypass pathway that allows oxidation of methanol to the level of methylene-H4MPT in M. barkeri. The data further suggested that formaldehyde may be an intermediate in this bypass; however, no methanol dehydrogenase activity was found in Δmtr cell extracts, nor was there an obligate role for the formaldehyde-activating enzyme (Fae), which has been shown to catalyze the condensation of formaldehyde and H4MPT in vitro. Both the Δmer and Δmtr mutants were able to grow on a combination of methanol plus acetate, but they did so by metabolic pathways that are clearly distinct from each other and from previously characterized methanogenic pathways.

scholarly journals Adaptation of Corynebacterium glutamicum to Ammonium Limitation: a Global Analysis Using Transcriptome and Proteome Techniques

2005 ◽  
Vol 71 (5) ◽  
pp. 2391-2402 ◽  
Author(s):  
Maike Silberbach ◽  
Mathias Schäfer ◽  
Andrea T. Hüser ◽  
Jörn Kalinowski ◽  
Alfred Pühler ◽  
...  
Keyword(s):  
Corynebacterium Glutamicum ◽  
Metabolic Pathways ◽  
Ribosomal Proteins ◽  
Nitrogen Assimilation ◽  
Global Analysis ◽  
Cellular Transport ◽  
Acid Biosynthesis ◽  
Limited Growth ◽  
Rate Dependent ◽  
Genes Encoding

ABSTRACT Theresponse of Corynebacterium glutamicum to ammonium limitation was studied by transcriptional and proteome profiling of cells grown in a chemostat. Our results show that ammonium-limited growth of C. glutamicum results in a rearrangement of the cellular transport capacity, changes in metabolic pathways for nitrogen assimilation, amino acid biosynthesis, and carbon metabolism, as well as a decreased cell division. Since transcription at different growth rates was studied, it was possible to distinguish specific responses to ammonium limitation and more general, growth rate-dependent alterations in gene expression. The latter include a number of genes encoding ribosomal proteins and genes for FoF1-ATP synthase subunits.

scholarly journals Fatty Acid Synthesis and Pyruvate Metabolism Pathways Remain Active in Dihydroartemisinin-Induced Dormant Ring Stages of Plasmodium falciparum

2014 ◽  
Vol 58 (8) ◽  
pp. 4773-4781 ◽  
Author(s):  
Nanhua Chen ◽  
Alexis N. LaCrue ◽  
Franka Teuscher ◽  
Norman C. Waters ◽  
Michelle L. Gatton ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Fatty Acid Synthesis ◽  
Metabolic Pathways ◽  
Acid Synthesis ◽  
High Rate ◽  
Mitochondrial Proteins ◽  
Pyruvate Metabolism ◽  
Transcription Analysis ◽  
Recent Emergence ◽  
Genes Encoding

ABSTRACTArtemisinin (ART)-based combination therapy (ACT) is used as the first-line treatment of uncomplicated falciparum malaria worldwide. However, despite high potency and rapid action, there is a high rate of recrudescence associated with ART monotherapy or ACT long before the recent emergence of ART resistance. ART-induced ring-stage dormancy and recovery have been implicated as possible causes of recrudescence; however, little is known about the characteristics of dormant parasites, including whether dormant parasites are metabolically active. We investigated the transcription of 12 genes encoding key enzymes in various metabolic pathways inP. falciparumduring dihydroartemisinin (DHA)-induced dormancy and recovery. Transcription analysis showed an immediate downregulation for 10 genes following exposure to DHA but continued transcription of 2 genes encoding apicoplast and mitochondrial proteins. Transcription of several additional genes encoding apicoplast and mitochondrial proteins, particularly of genes encoding enzymes in pyruvate metabolism and fatty acid synthesis pathways, was also maintained. Additions of inhibitors for biotin acetyl-coenzyme A (CoA) carboxylase and enoyl-acyl carrier reductase of the fatty acid synthesis pathways delayed the recovery of dormant parasites by 6 and 4 days, respectively, following DHA treatment. Our results demonstrate that most metabolic pathways are downregulated in DHA-induced dormant parasites. In contrast, fatty acid and pyruvate metabolic pathways remain active. These findings highlight new targets to interrupt recovery of parasites from ART-induced dormancy and to reduce the rate of recrudescence following ART treatment.

Layer-specific differences of gene expression in extraocular muscles identified by laser-capture microscopy

2004 ◽  
Vol 20 (1) ◽  
pp. 55-65 ◽  
Author(s):  
Murat T. Budak ◽  
Sasha Bogdanovich ◽  
Martin H. J. Wiesen ◽  
Olga Lozynska ◽  
Tejvir S. Khurana ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Extraocular Muscles ◽  
Molecular Evidence ◽  
Structural Elements ◽  
Evolutionary Mechanisms ◽  
Functional Roles ◽  
Laser Capture Microscopy ◽  
Vascular Elements ◽  
Genes Encoding ◽  
Laser Capture

In mammals, separate muscles are typically specialized as a whole to provide distinct functional roles leading to well-recognized adaptations. This is exemplified in the lower limb by the slow, fatigue-resistant soleus, which provides a postural role vs. the fast, fatiguable tibialis anterior (TA), which provides rapid movements. A unique characteristic of extraocular muscles (EOMs) is their compartmentalization into two distinct layers, the orbital layer (OL) and global layer (GL), presumably to subserve diverse functions within the same muscle. However, molecular evidence of this diversity has been limited. We used laser-capture microscopy coupled with microarray-based expression profiling to identify molecular differences between the OL and GL of rat EOMs. We found that 210 genes were differentially regulated between these layers at a twofold expression cutoff. Differences in genes related to metabolic pathways and related to structural elements of muscle and nerve formed the largest functional clusters. Layer-specific differential expression was validated at both mRNA and protein level for MYH3, MYH6, and ACTN3. The expected layer-specific differences among genes encoding vascular elements were not evident by profiling; morphometric analysis demonstrated that the differences exist, but at a magnitude below the cutoff level established by our statistical methods. Comparison of these results with previous results comparing whole EOMs and TA suggest evolutionary mechanisms may play a role in achieving functional distinctions between OL and GL.

Analysis of genetic diversity inCitrus

2011 ◽  
Vol 9 (2) ◽  
pp. 218-221 ◽  
Author(s):  
François Luro ◽  
Julia Gatto ◽  
Gilles Costantino ◽  
Olivier Pailly
Keyword(s):  
Genetic Diversity ◽  
Organic Acids ◽  
Metabolic Pathways ◽  
Single Strand Conformation Polymorphism ◽  
Strongly Correlated ◽  
Cultivation Conditions ◽  
Citrus Pulp ◽  
Genes Encoding ◽  
Citrus Juices ◽  
Conformation Polymorphism

Sugar and acidity levels are the main criteria of general fruit quality and for citrus juices pulp, in particular. The constituents of the acidity (organic acids) and the sweetness (glucose, fructose and sucrose) and the genes involved in their regulation have seldom been used to exploreCitrusgenetic diversity. We evaluated the juice composition of primary metabolic components for 87 varieties belonging to the eight majorCitrusspecies grown under the same environmental and cultivation conditions by HPLC. We investigated the sequence polymorphism of nine candidate genes encoding for key enzymes of sugars and organic acids metabolic pathways by single strand conformation polymorphism (SSCP). Whatever the biochemical or molecular analyses, the observed structure ofCitrusdiversity was organized around three groups corresponding to the ancestral species (mandarin, pummelo and citron). As expected, the secondary species were closely related to their putative ancestors except forCitrus aurantium. Biochemical diversity was strongly correlated to molecular SSCP diversity at the genus level but not at the intraspecific level. Compared with other molecular marker types, higher diversity has been observed with SSCP technology, which makes it suitable for future quantitative trait loci mapping approach on gene polymorphism in citrus pulp acidity and sweetness regulation.

scholarly journals The In Vivo Transcriptomic Blueprint of Mycobacterium tuberculosis in the Lung

2021 ◽  
Vol 12 ◽  
Author(s):  
Mariateresa Coppola ◽  
Rachel P-J. Lai ◽  
Robert J. Wilkinson ◽  
Tom H. M. Ottenhoff
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Metabolic Pathways ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Genes Encoding ◽  
High Concordance ◽  
Lower Correlation

Mycobacterium tuberculosis (Mtb) genes encoding proteins targeted by vaccines and drugs should be expressed in the lung, the main organ affected by Mtb, for these to be effective. However, the pulmonary expression of most Mtb genes and their proteins remains poorly characterized. The aim of this study is to fill this knowledge gap. We analyzed large scale transcriptomic datasets from specimens of Mtb-infected humans, TB-hypersusceptible (C3H/FeJ) and TB-resistant (C57BL/6J) mice and compared data to in vitro cultured Mtb gene-expression profiles. Results revealed high concordance in the most abundantly in vivo expressed genes between pulmonary Mtb transcriptomes from different datasets and different species. As expected, this contrasted with a lower correlation found with the highest expressed Mtb genes from in vitro datasets. Among the most consistently and highly in vivo expressed genes, 35 have not yet been explored as targets for vaccination or treatment. More than half of these genes are involved in protein synthesis or metabolic pathways. This first lung-oriented multi-study analysis of the in vivo expressed Mtb-transcriptome provides essential data that considerably increase our understanding of pulmonary TB infection biology, and identifies novel molecules for target-based TB-vaccine and drug development.

scholarly journals Vanillic acid and methoxyhydroquinone production from guaiacyl units and related aromatic compounds using Aspergillus niger cell factories

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Ronnie J. M. Lubbers ◽  
Adiphol Dilokpimol ◽  
Paula A. Nousiainen ◽  
Răzvan C. Cioc ◽  
Jaap Visser ◽  
...  
Keyword(s):  
Aspergillus Niger ◽  
Metabolic Pathway ◽  
Vanillic Acid ◽  
Aromatic Compounds ◽  
Metabolic Pathways ◽  
Fungal Cell ◽  
Cell Factories ◽  
Genes Encoding ◽  
Pharmaceutical Industries ◽  
Guaiacyl Lignin

Abstract Background The aromatic compounds vanillin and vanillic acid are important fragrances used in the food, beverage, cosmetic and pharmaceutical industries. Currently, most aromatic compounds used in products are chemically synthesized, while only a small percentage is extracted from natural sources. The metabolism of vanillin and vanillic acid has been studied for decades in microorganisms and many studies have been conducted that showed that both can be produced from ferulic acid using bacteria. In contrast, the degradation of vanillin and vanillic acid by fungi is poorly studied and no genes involved in this metabolic pathway have been identified. In this study, we aimed to clarify this metabolic pathway in Aspergillus niger and identify the genes involved. Results Using whole-genome transcriptome data, four genes involved in vanillin and vanillic acid metabolism were identified. These include vanillin dehydrogenase (vdhA), vanillic acid hydroxylase (vhyA), and two genes encoding novel enzymes, which function as methoxyhydroquinone 1,2-dioxygenase (mhdA) and 4-oxo-monomethyl adipate esterase (omeA). Deletion of these genes in A. niger confirmed their role in aromatic metabolism and the enzymatic activities of these enzymes were verified. In addition, we demonstrated that mhdA and vhyA deletion mutants can be used as fungal cell factories for the accumulation of vanillic acid and methoxyhydroquinone from guaiacyl lignin units and related aromatic compounds. Conclusions This study provides new insights into the fungal aromatic metabolic pathways involved in the degradation of guaiacyl units and related aromatic compounds. The identification of the involved genes unlocks new potential for engineering aromatic compound-producing fungal cell factories.

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