scholarly journals Comparative analysis of Lysine and Arginine biosynthesis pathway in Deinococcus genomes

2021 ◽  
Author(s):  
Sankar Mahesh ◽  
Deepa Sethi ◽  
Richa Priyadarshini ◽  
Ragothaman M Yennamalli
Keyword(s):  
Cell Envelope ◽  
Glutamate Synthase ◽  
Optimal Level ◽  
Lysine Biosynthesis ◽  
Divergent Evolution ◽  
Structural Level ◽  
Biosynthesis Pathway ◽  
Arginine Biosynthesis ◽  
Structural Variations ◽  
Lysine Deacetylase

The members of the Deinococcaceae family have the ability to survive extreme environmental conditions. Deinococcus species have a complex cell envelope composed of L-ornithine containing peptidoglycan. Anabolism of L-ornithine is intrinsically linked to L-lysine and L-arginine biosynthetic pathways. To understand these two pathways, we analyzed the L-lysine and L-arginine pathways using 23 Deinococcus genomes, including D. indicus. We used BLAST-P based ortholog identification using D. radiodurans genes as the query. We identified some BLAST-P hits that shared the same functional annotation. We analyzed three (class I aminotransferase, acetyl-lysine deacetylase, and acetyl glutamate/acetyl aminoadipate kinase) from L-lysine biosynthesis pathway and three (bifunctional ornithine acetyltransferase or N-acetyl glutamate synthase protein, nitric oxide synthase-like protein, and Acetyl-lysine deacetylase) from L-arginine biosynthesis pathway. Two proteins showed certain structural variations. Specifically, [LysW]-lysine hydrolase protein sequence and structure level changes indicated changes in oligomeric conformation, which could likely be a result of divergent evolution. And, bifunctional ornithine acetyltransferase or N-acetyl glutamate synthase had its active site pocket positions shifted at the structural level and we hypothesize that it may not perform at the optimal level. Thus, we were able to compare and contrast different Deinococcus species indicating some genes occurring because of divergent evolution.

scholarly journals Bayesian Network Analysis of Lysine Biosynthesis Pathway in Rice

Inventions ◽  
2021 ◽  
Vol 6 (2) ◽  
pp. 37
Author(s):  
Aditya Lahiri ◽  
Khushboo Rastogi ◽  
Aniruddha Datta ◽  
Endang M. Septiningsih
Keyword(s):  
Amino Acids ◽  
Reporter Gene ◽  
Nacl Stress ◽  
Stress Conditions ◽  
Lysine Biosynthesis ◽  
Model Parameters ◽  
Saline Stress ◽  
Lysine Content ◽  
Biosynthesis Pathway ◽  
Healthy Functioning

Lysine is the first limiting essential amino acid in rice because it is present in the lowest quantity compared to all the other amino acids. Amino acids are the building block of proteins and play an essential role in maintaining the human body’s healthy functioning. Rice is a staple food for more than half of the global population; thus, increasing the lysine content in rice will help improve global health. In this paper, we studied the lysine biosynthesis pathway in rice (Oryza sativa) to identify the regulators of the lysine reporter gene LYSA (LOC_Os02g24354). Genetically intervening at the regulators has the potential to increase the overall lysine content in rice. We modeled the lysine biosynthesis pathway in rice seedlings under normal and saline (NaCl) stress conditions using Bayesian networks. We estimated the model parameters using experimental data and identified the gene DAPF(LOC_Os12g37960) as a positive regulator of the lysine reporter gene LYSA under both normal and saline stress conditions. Based on this analysis, we conclude that the gene DAPF is a potent candidate for genetic intervention. Upregulating DAPF using methods such as CRISPR-Cas9 gene editing strategy has the potential to upregulate the lysine reporter gene LYSA and increase the overall lysine content in rice.

scholarly journals Arginine-deprivation–induced oxidative damage sterilizes Mycobacterium tuberculosis

2018 ◽  
Vol 115 (39) ◽  
pp. 9779-9784 ◽  
Author(s):  
Sangeeta Tiwari ◽  
Andries J. van Tonder ◽  
Catherine Vilchèze ◽  
Vitor Mendes ◽  
Sherine E. Thomas ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Dna Damage ◽  
Mycobacterium Tuberculosis ◽  
De Novo ◽  
Target Space ◽  
Biosynthesis Pathway ◽  
Arginine Biosynthesis ◽  
Arginine Deprivation

Reactive oxygen species (ROS)-mediated oxidative stress and DNA damage have recently been recognized as contributing to the efficacy of most bactericidal antibiotics, irrespective of their primary macromolecular targets. Inhibitors of targets involved in both combating oxidative stress as well as being required for in vivo survival may exhibit powerful synergistic action. This study demonstrates that the de novo arginine biosynthetic pathway in Mycobacterium tuberculosis (Mtb) is up-regulated in the early response to the oxidative stress-elevating agent isoniazid or vitamin C. Arginine deprivation rapidly sterilizes the Mtb de novo arginine biosynthesis pathway mutants ΔargB and ΔargF without the emergence of suppressor mutants in vitro as well as in vivo. Transcriptomic and flow cytometry studies of arginine-deprived Mtb have indicated accumulation of ROS and extensive DNA damage. Metabolomics studies following arginine deprivation have revealed that these cells experienced depletion of antioxidant thiols and accumulation of the upstream metabolite substrate of ArgB or ArgF enzymes. ΔargB and ΔargF were unable to scavenge host arginine and were quickly cleared from both immunocompetent and immunocompromised mice. In summary, our investigation revealed in vivo essentiality of the de novo arginine biosynthesis pathway for Mtb and a promising drug target space for combating tuberculosis.

scholarly journals Novel Strategies for Genomic Manipulation of Trichoderma reesei with the Purpose of Strain Engineering

2015 ◽  
Vol 81 (18) ◽  
pp. 6314-6323 ◽  
Author(s):  
Christian Derntl ◽  
Daniel P. Kiesenhofer ◽  
Robert L. Mach ◽  
Astrid R. Mach-Aigner
Keyword(s):  
Trichoderma Reesei ◽  
Marker Gene ◽  
Strain Engineering ◽  
Lysine Biosynthesis ◽  
Transformation Rate ◽  
Biosynthesis Pathway ◽  
Transformation System ◽  
Reporter System ◽  
Content Type ◽  
Gene Insertion

ABSTRACTThe state-of-the-art procedure for gene insertions intoTrichoderma reeseiis a cotransformation of two plasmids, one bearing the gene of interest and the other a marker gene. This procedure yields up to 80% transformation efficiency, but both the number of integrated copies and the loci of insertion are unpredictable. This can lead to tremendous pleiotropic effects. This study describes the development of a novel transformation system for site-directed gene insertion based on auxotrophic markers. For this purpose, we tested the applicability of the genesasl1(encoding an enzyme of thel-arginine biosynthesis pathway), thehah1(encoding an enzyme of thel-lysine biosynthesis pathway), and thepyr4(encoding an enzyme of the uridine biosynthesis pathway). The developed transformation system yields strains with an additional gene at a defined locus that are prototrophic and ostensibly isogenic compared to their parental strain. A positive transformation rate of 100% was achieved due to the developed split-marker system. Additionally, a double-auxotrophic strain that allows multiple genomic manipulations was constructed, which facilitates metabolic engineering purposes inT. reesei. By employinggoxAofAspergillus nigeras a reporter system, the influence on the expression of an inserted gene caused by the orientation of the insertion and the transformation strategy used could be demonstrated. Both are important aspects to be considered during strain engineering.

scholarly journals Mutations in the Lipopolysaccharide Biosynthesis Pathway Interfere with Crescentin-Mediated Cell Curvature in Caulobacter crescentus

2010 ◽  
Vol 192 (13) ◽  
pp. 3368-3378 ◽  
Author(s):  
Matthew T. Cabeen ◽  
Michelle A. Murolo ◽  
Ariane Briegel ◽  
N. Khai Bui ◽  
Waldemar Vollmer ◽  
...  
Keyword(s):  
Cell Wall ◽  
Caulobacter Crescentus ◽  
Cell Envelope ◽  
Cellular Systems ◽  
Biosynthesis Pathway ◽  
Cell Morphogenesis ◽  
Division Site ◽  
Growth Properties ◽  
A Cell ◽  
Cellular Components

ABSTRACT Bacterial cell morphogenesis requires coordination among multiple cellular systems, including the bacterial cytoskeleton and the cell wall. In the vibrioid bacterium Caulobacter crescentus, the intermediate filament-like protein crescentin forms a cell envelope-associated cytoskeletal structure that controls cell wall growth to generate cell curvature. We undertook a genetic screen to find other cellular components important for cell curvature. Here we report that deletion of a gene (wbqL) involved in the lipopolysaccharide (LPS) biosynthesis pathway abolishes cell curvature. Loss of WbqL function leads to the accumulation of an aberrant O-polysaccharide species and to the release of the S layer in the culture medium. Epistasis and microscopy experiments show that neither S-layer nor O-polysaccharide production is required for curved cell morphology per se but that production of the altered O-polysaccharide species abolishes cell curvature by apparently interfering with the ability of the crescentin structure to associate with the cell envelope. Our data suggest that perturbations in a cellular pathway that is itself fully dispensable for cell curvature can cause a disruption of cell morphogenesis, highlighting the delicate harmony among unrelated cellular systems. Using the wbqL mutant, we also show that the normal assembly and growth properties of the crescentin structure are independent of its association with the cell envelope. However, this envelope association is important for facilitating the local disruption of the stable crescentin structure at the division site during cytokinesis.

scholarly journals ArgR and AhrC Are Both Required for Regulation of Arginine Metabolism in Lactococcus lactis

2004 ◽  
Vol 186 (4) ◽  
pp. 1147-1157 ◽  
Author(s):  
Rasmus Larsen ◽  
Girbe Buist ◽  
Oscar P. Kuipers ◽  
Jan Kok
Keyword(s):  
Lactococcus Lactis ◽  
Double Mutant ◽  
Protein Complexes ◽  
Dna Binding Proteins ◽  
Unique Property ◽  
Deletion Mutants ◽  
Biosynthesis Pathway ◽  
Arginine Metabolism ◽  
Arginine Biosynthesis ◽  
Arginine Catabolism

ABSTRACT The DNA binding proteins ArgR and AhrC are essential for regulation of arginine metabolism in Escherichia coli and Bacillus subtilis, respectively. A unique property of these regulators is that they form hexameric protein complexes, mediating repression of arginine biosynthetic pathways as well as activation of arginine catabolic pathways. The gltS-argE operon of Lactococcus lactis encodes a putative glutamate or arginine transport protein and acetylornithine deacetylase, which catalyzes an important step in the arginine biosynthesis pathway. By random integration knockout screening we found that derepression mutants had ISS1 integrations in, among others, argR and ahrC. Single as well as double regulator deletion mutants were constructed from Lactococcus lactis subsp. cremoris MG1363. The three arginine biosynthetic operons argCJDBF, argGH, and gltS-argE were shown to be repressed by the products of argR and ahrC. Furthermore, the arginine catabolic arcABD1C1C2TD2 operon was activated by the product of ahrC but not by that of argR. Expression from the promoter of the argCJDBF operon reached similar levels in the single mutants and in the double mutant, suggesting that the regulators are interdependent and not able to complement each other. At the same time they also appear to have different functions, as only AhrC is involved in activation of arginine catabolism. This is the first study where two homologous arginine regulators are shown to be involved in arginine regulation in a prokaryote, representing an unusual mechanism of regulation.

scholarly journals Importance of Lipopolysaccharide and Cyclicβ-1,2-Glucans inBrucella-Mammalian Infections

2010 ◽  
Vol 2010 ◽  
pp. 1-12 ◽  
Author(s):  
Andreas F. Haag ◽  
Kamila K. Myka ◽  
Markus F. F. Arnold ◽  
Paola Caro-Hernández ◽  
Gail P. Ferguson
Keyword(s):  
Immune System ◽  
Vaccine Development ◽  
Cell Envelope ◽  
Zoonotic Diseases ◽  
Innate Immune ◽  
Economic Losses ◽  
Biosynthesis Pathway ◽  
Host Interaction ◽  
Causative Agents

Brucellaspecies are the causative agents of one of the most prevalent zoonotic diseases: brucellosis. Infections byBrucellaspecies cause major economic losses in agriculture, leading to abortions in infected animals and resulting in a severe, although rarely lethal, debilitating disease in humans.Brucellaspecies persist as intracellular pathogens that manage to effectively evade recognition by the host's immune system. Sugar-modified components in theBrucellacell envelope play an important role in their host interaction.Brucellalipopolysaccharide (LPS), unlikeEscherichia coliLPS, does not trigger the host's innate immune system.Brucellaproduces cyclicβ-1,2-glucans, which are important for targeting them to their replicative niche in the endoplasmic reticulum within the host cell. This paper will focus on the role of LPS and cyclicβ-1,2-glucans inBrucella-mammalian infections and discuss the use of mutants, within the biosynthesis pathway of these cell envelope structures, in vaccine development.

scholarly journals An ll-Diaminopimelate Aminotransferase Defines a Novel Variant of the Lysine Biosynthesis Pathway in Plants

2005 ◽  
Vol 140 (1) ◽  
pp. 292-301 ◽  
Author(s):  
André O. Hudson ◽  
Bijay K. Singh ◽  
Thomas Leustek ◽  
Charles Gilvarg
Keyword(s):  
Lysine Biosynthesis ◽  
Biosynthesis Pathway ◽  
Novel Variant
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