scholarly journals Cloning and characterization of cobA, one of vitamin B12 biosynthesis pathway genes from Selenomonas ruminantium

2021 ◽  
Vol 10 (2) ◽  
pp. 131-135
Author(s):  
Lívia Fecskeová ◽  
Peter Pristaš ◽  
Peter Javorský
Keyword(s):  
Amino Acid ◽  
Vitamin B12 ◽  
Biosynthetic Pathway ◽  
Anaerobic Bacteria ◽  
Protein Sequences ◽  
Synthesis Process ◽  
Biosynthesis Pathway ◽  
Selenomonas Ruminantium ◽  
Main Producer

Bacterial biosynthesis of vitamin B12 can occur via either aerobic or anaerobic route. While the aerobic pathway has been fully elucidated and understood, less is known about the anaerobic pathway. Selenomonas ruminantium is thought to be the main producer of this vitamin in rumen environment and must use the anaerobic pathway. In our work we found one of the genes of vitamin B12 biosynthetic pathway of S. ruminantium, encoding for the cobalamin adenosyltransferase, enzyme taking part at the last steps of the synthesis process. Deduced amino acid sequence showed the highest similarity to cobalamin adenosyltransferases of other ruminal anaerobic bacteria and that of species Selenomonas. Phylogenetic comparisons of CobA protein sequences of several anaerobic bacteria of Clostridiale order indicate possible horizontal transfer of this gene.

scholarly journals Genetic Characterization of the Carotenoid Biosynthetic Pathway in Methylobacterium extorquens AM1 and Isolation of a Colorless Mutant

2003 ◽  
Vol 69 (12) ◽  
pp. 7563-7566 ◽  
Author(s):  
Stephen J. Van Dien ◽  
Christopher J. Marx ◽  
Brooke N. O'Brien ◽  
Mary E. Lidstrom
Keyword(s):  
Biosynthetic Pathway ◽  
Genetic Characterization ◽  
Carotenoid Biosynthesis ◽  
Biosynthesis Pathway ◽  
Wild Type ◽  
Methylobacterium Extorquens ◽  
Growth Properties ◽  
Carotenoid Biosynthesis Pathway ◽  
Free Strain

ABSTRACT Genomic searches were used to reconstruct the putative carotenoid biosynthesis pathway in the pink-pigmented facultative methylotroph Methylobacterium extorquens AM1. Four genes for putative phytoene desaturases were identified. A colorless mutant was obtained by transposon mutagenesis, and the insertion was shown to be in one of the putative phytoene desaturase genes. Mutations in the other three did not affect color. The tetracycline marker was removed from the original transposon mutant, resulting in a pigment-free strain with wild-type growth properties useful as a tool for future experiments.

scholarly journals Characterization of the Enzyme CbiH60Involved in Anaerobic Ring Contraction of the Cobalamin (Vitamin B12) Biosynthetic Pathway

2012 ◽  
Vol 288 (1) ◽  
pp. 297-305 ◽  
Author(s):  
Simon J. Moore ◽  
Rebekka Biedendieck ◽  
Andrew D. Lawrence ◽  
Evelyne Deery ◽  
Mark J. Howard ◽  
...  
Keyword(s):  
Vitamin B12 ◽  
Biosynthetic Pathway ◽  
Ring Contraction

Anaerobic synthesis of vitamin B12: characterization of the early steps in the pathway

2005 ◽  
Vol 33 (4) ◽  
pp. 811-814 ◽  
Author(s):  
S. Frank ◽  
A.A. Brindley ◽  
E. Deery ◽  
P. Heathcote ◽  
A.D. Lawrence ◽  
...  
Keyword(s):  
Vitamin B12 ◽  
Biosynthetic Pathway ◽  
Recent Progress ◽  
Recombinant Dna ◽  
Structural Studies ◽  
Recombinant Dna Technology ◽  
Factor Ii ◽  
Dna Technology ◽  
Insight Into

The anaerobic biosynthesis of vitamin B12 is slowly being unravelled. Recent work has shown that the first committed step along the anaerobic route involves the sirohydrochlorin (chelation of cobalt into factor II). The following enzyme in the pathway, CbiL, methylates cobalt-factor II to give cobalt-factor III. Recent progress on the molecular characterization of this enzyme has given a greater insight into its mode of action and specificity. Structural studies are being used to provide insights into how aspects of this highly complex biosynthetic pathway may have evolved. Between cobalt-factor III and cobyrinic acid, only one further intermediate has been identified. A combination of molecular genetics, recombinant DNA technology and bioorganic chemistry has led to some recent advances in assigning functions to the enzymes of the anaerobic pathway.

scholarly journals Novel Numerical Characterization of Protein Sequences Based on Individual Amino Acid and Its Application

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Yan-ping Zhang ◽  
Ya-jun Sheng ◽  
Wei Zheng ◽  
Ping-an He ◽  
Ji-shuo Ruan
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Catalytic Mechanism ◽  
Graphical Representation ◽  
Sequence Similarity ◽  
Protein Sequences ◽  
Numerical Characteristic ◽  
Individual Amino Acid ◽  
Numerical Characterization

The hydrophobicity and hydrophilicity of amino acids play a very important role in protein folding and its interaction with the environment and other molecules, as well as its catalytic mechanism. Based on the two physicochemical indexes, a 2D graphical representation of protein sequences is introduced; meanwhile, a new numerical characteristic has been proposed to compute the distance of different sequences for analysis of sequence similarity/dissimilarity on the basis of this graphical representation. Furthermore, we apply the new distance in the similarities/dissimilarities of ND5 proteins of nine species and predict the four major classes based on the dataset containing 639 domains. The results show that the method is simple and effective.

scholarly journals Mathematical Characterization of Protein Transmembrane Regions

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Amrita Roy Choudhury ◽  
Nikolay Zhukov ◽  
Marjana Novič
Keyword(s):  
Amino Acid ◽  
Adjacency Matrix ◽  
Protein Sequences ◽  
Evolutionary Information ◽  
Sequence Information ◽  
Physiochemical Properties ◽  
Novel Method ◽  
Encoding Protein

Graphical bioinformatics has paved a unique way of mathematical characterization of proteins and proteomic maps. The graphics representations and the corresponding mathematical descriptors have proved to be useful and have provided unique solutions to problems related to identification, comparisons, and analyses of protein sequences and proteomics maps. Based on sequence information alone, these descriptors are independent from physiochemical properties of amino acids and evolutionary information. In this work, we have presented invariants from amino acid adjacency matrix and decagonal isometries matrix as potential descriptors of protein sequences. Encoding protein sequences into amino acid adjacency matrix is already well established. We have shown its application in classification of transmembrane and nontransmembrane regions of membrane protein sequences. We have introduced the dodecagonal isometries matrix, which is a novel method of encoding protein sequences based on decagonal isometries group.

scholarly journals Genome-wide characterization of the MLO gene family in Cannabis sativa reveals two genes as strong candidates for powdery mildew susceptibility

2021 ◽  
Author(s):  
Noémi Pépin ◽  
Francois Olivier Hebert ◽  
David L Joly
Keyword(s):  
Amino Acid ◽  
Powdery Mildew ◽  
Gene Family ◽  
Cannabis Sativa ◽  
Protein Sequences ◽  
Cultivated Plants ◽  
Economic Losses ◽  
Functional Domain ◽  
Wide Range

Cannabis sativa is increasingly being grown around the world for medicinal, industrial, and recreational purposes. As in all cultivated plants, cannabis is exposed to a wide range of pathogens, including powdery mildew (PM). This fungal disease stresses cannabis plants and reduces flower bud quality, resulting in significant economic losses for licensed producers. The Mildew Locus O (MLO) gene family encodes plant-specific proteins distributed among conserved clades, of which clades IV and V are known to be involved in susceptibility to PM in monocots and dicots, respectively. In several studies, the inactivation of those genes resulted in durable resistance to the disease. In this study, we identified and characterized the MLO gene family members in five different cannabis genomes. Fifteen Cannabis sativa MLO (CsMLO) genes were manually curated in cannabis, with numbers varying between 14, 17, 19, 18, and 18 for CBDRx, Jamaican Lion female, Jamaican Lion male, Purple Kush, and Finola, respectively (when considering paralogs and incomplete genes). Further analysis of the CsMLO genes and their deduced protein sequences revealed that many characteristics of the gene family, such as the presence of 7 transmembrane domains, the MLO functional domain, and particular amino acid positions, were present and well conserved. Phylogenetic analysis of the MLO protein sequences from all five cannabis genomes and other plant species indicated seven distinct clades (I through VII), as reported in other crops. Expression analysis revealed that the CsMLOs from clade V, CsMLO1 and CsMLO4, were significantly upregulated following Golovinomyces ambrosiae infection, providing preliminary evidence that they could be involved in PM susceptibility. Finally, the examination of variation within CsMLO1 and CsMLO4 in 32 cannabis cultivars revealed several amino acid changes, which could affect their function. Altogether, cannabis MLO genes were identified and characterized, among which candidates potentially involved in PM susceptibility were noted. The results of this study will lay the foundation for further investigations, such as the functional characterization of clade V MLOs as well as the potential impact of the amino acid changes reported. Those will be useful for breeding purposes in order to develop resistant cultivars.

scholarly journals Genome-Wide Characterization of the MLO Gene Family in Cannabis sativa Reveals Two Genes as Strong Candidates for Powdery Mildew Susceptibility

2021 ◽  
Vol 12 ◽  
Author(s):  
Noémi Pépin ◽  
Francois Olivier Hebert ◽  
David L. Joly
Keyword(s):  
Amino Acid ◽  
Powdery Mildew ◽  
Gene Family ◽  
Cannabis Sativa ◽  
Protein Sequences ◽  
Cultivated Plants ◽  
Economic Losses ◽  
Functional Domain ◽  
Wide Range

Cannabis sativa is increasingly being grown around the world for medicinal, industrial, and recreational purposes. As in all cultivated plants, cannabis is exposed to a wide range of pathogens, including powdery mildew (PM). This fungal disease stresses cannabis plants and reduces flower bud quality, resulting in significant economic losses for licensed producers. The Mildew Locus O (MLO) gene family encodes plant-specific proteins distributed among conserved clades, of which clades IV and V are known to be involved in susceptibility to PM in monocots and dicots, respectively. In several studies, the inactivation of those genes resulted in durable resistance to the disease. In this study, we identified and characterized the MLO gene family members in five different cannabis genomes. Fifteen Cannabis sativa MLO (CsMLO) genes were manually curated in cannabis, with numbers varying between 14, 17, 19, 18, and 18 for CBDRx, Jamaican Lion female, Jamaican Lion male, Purple Kush, and Finola, respectively (when considering paralogs and incomplete genes). Further analysis of the CsMLO genes and their deduced protein sequences revealed that many characteristics of the gene family, such as the presence of seven transmembrane domains, the MLO functional domain, and particular amino acid positions, were present and well conserved. Phylogenetic analysis of the MLO protein sequences from all five cannabis genomes and other plant species indicated seven distinct clades (I through VII), as reported in other crops. Expression analysis revealed that the CsMLOs from clade V, CsMLO1 and CsMLO4, were significantly upregulated following Golovinomyces ambrosiae infection, providing preliminary evidence that they could be involved in PM susceptibility. Finally, the examination of variation within CsMLO1 and CsMLO4 in 32 cannabis cultivars revealed several amino acid changes, which could affect their function. Altogether, cannabis MLO genes were identified and characterized, among which candidates potentially involved in PM susceptibility were noted. The results of this study will lay the foundation for further investigations, such as the functional characterization of clade V MLOs as well as the potential impact of the amino acid changes reported. Those will be useful for breeding purposes in order to develop resistant cultivars.

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