Touraj Rahimi; Ali Niazi; Seyed Mohsen Taghavi; Esmaeil Ebrahimie; Shahab Ayatollahi; Tahereh Deihimi
Abstract
The isolation of native microorganism that produced biosurfactants in order to oil pollutants bioremediation and hydrophobic oil hydrocarbons availability inter soil texture has become important issues in bioremediation technology. Surfactin is one of the biosurfactants with more application that produced ...
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The isolation of native microorganism that produced biosurfactants in order to oil pollutants bioremediation and hydrophobic oil hydrocarbons availability inter soil texture has become important issues in bioremediation technology. Surfactin is one of the biosurfactants with more application that produced by Bacillus subtilis strains could overcome these problems. Thus in this study, we investigated operon which involved in surfactin biosynthesis and its regulator comQXPA operon due to a high level of surfactin biosynthesis by B. subtilis MJ01 isolated from oil contaminated soil based on comparative genomics approaches. Surfactin operon localized and compared among six genomes of close relative strains and MJ01 indicated that missense point mutations on genes of surfactin operon were existence. These mutations affected NPRS protein AMP-binding domain that responsible to bind amino acid to correct the situation on surfactin peptide ring. It seems that lack of hemolytic and anti-microbial function of MJ01 surfactin was due to the creation of missense mutation and modifications in the surfactin biosynthesis NPRS enzyme structure. Moreover, srf genes expression regulated by comQXPA quorum sensing operon. MJ01 Quorum sensing operon rearrangement showed that part of the comQ gene was extended into comX gene and these genes had overlap region. Results suggested that in MJ01 genome has been occurred specific combination of QS genes organization. Despite high similarity of three genes comQXP among MJ01 with BEST7613 and other subtilis strains group, comA gene showed high identity with spizizenii strains group.
Tahereh Deihimi; Esmaeil Ebrahimie; Ali Niazi; Mansour Ebrahimi; Shahab Ayatollahi; Ahmad Tahmasebi; Touraj Rahimi; Moein Jahanbani Veshareh
Abstract
Applying microorganism in oil recovery has attracted attentions recently. Surfactin produced by Bacillus subtilis is widely used industrially in a range of industrial applications in pharmecutical and environmental sectors. Little information about molecular mechanism of suffactin compound is available. ...
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Applying microorganism in oil recovery has attracted attentions recently. Surfactin produced by Bacillus subtilis is widely used industrially in a range of industrial applications in pharmecutical and environmental sectors. Little information about molecular mechanism of suffactin compound is available. In this study, we performed promoter and network analysis of surfactin production genes in Bacillus subtilis subsp. MJ01 (isolated from oil contaminated soil in South of Iran), spizizenii and 168. Our analysis revealed that comQ and comX are the genes with sequence alterations among these three strains of Bacillus subtilis and are involved in surfactin production. Promoter analysis indicated that lrp, argR, rpoD, purr and ihf are overrepresented and have the highest number of transcription factor binding sites (TFBs) on the key surfactin production genes in all 3 strains. Also the pattern of TFBs among these three strains was completely different. Interestingly, there is distinct difference between 168, spizizenii and MJ01 in their frequency of TFs that activate genes involve in surfactin production. Attribute weighting algorithms and decision tree analysis revealed ihf, rpoD and flHCD as the most important TF among surfactin production. Network analysis identified two significant network modules. The first one consists of key genes involved in surfactin production and the second module includes key TFs, involved in regulation of surfactin production. Our findings enhance understanding the molecular mechanism of surfactin production through systems biology analysis.
Nassim Rahmani; Esmaeil Ebrahimie; Ali Niazi; Najaf Allahyari Fard; Bijan Bambai; Zarrin Minuchehr; Mansour Ebrahimi
Abstract
Allergens are proteins or glycoproteins which make widespread disorders that can lead to a systemic anaphylactic shock and even death within a short period of time. Understanding the protein features that are involved in allergenicity is important in developing future treatments as well as engineering ...
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Allergens are proteins or glycoproteins which make widespread disorders that can lead to a systemic anaphylactic shock and even death within a short period of time. Understanding the protein features that are involved in allergenicity is important in developing future treatments as well as engineering proteins in genetic transformation projects. A big dataset of 1439 protein features from 761 plant allergens and 7815 non-allergen proteins was constructed. Thereafter, 10 different attribute weighting algorithms were utilized to find the key characteristics differentiating allergens and non-allergen proteins. The frequency of Leu, Arg and Gln selected by different attribute weighting algorithms with more than 50% confidence, including attribute weighting by Weight_Info Gain, Weight Chi Squared, Weight_Gini Index and Weight_Relief. High amount of Gln and low percentage of Leu and Arg discriminate plant allergens from non-allergens
Sasan Mohsenzadeh; Sahar Sadeghi; Hassan Mohabatkar; Ali Niazi
Abstract
Osmotic stress is one of the major factors that significantly reduce yields in dry areas. Plants respond to this
abiotic stress at physiological and molecular levels. Many genes are induced under stress conditions by
transcription factors. Dehydration responsive element binding (DREB) protein is a ...
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Osmotic stress is one of the major factors that significantly reduce yields in dry areas. Plants respond to this
abiotic stress at physiological and molecular levels. Many genes are induced under stress conditions by
transcription factors. Dehydration responsive element binding (DREB) protein is a subfamily of AP2/ERF
transcription factors which control expression of many osmotic stress-inducible genes. In this study, 21 days
old seedlings of Sardari cultivar, dry farming bread wheat transferred into hydroponics culture using Hoagland
solution. Osmotic stress treatments performed with adding 100, 200 and 400 g/l poly-ethylene glycol 6000 to
hydroponics culture to obtain –0.15, –0.49, and –1.76 MPa water potential, respectively. After the seedlings
were withered and colorless, relative water content, dry weight, and photosynthesis measured. In addition, RTPCR,
and cDNA sequencing carried out. Molecular analysis of DREB translated protein sequence performed
by DNAMAN, BLASTN, Pfam and PROSITE software. Results showed that osmotic stress decreased relative
water content, root and shoot dry weight and net photosynthesis rate in comparison to control, significantly (P
< 0.05). Sequence alignment indicated 98% homology with other Triticum aestivum DREB protein mRNA.
There was an AP2 domain in the translated protein with three -sheets and one -helix and contains the Val14
and Glu19 amino acids. An EST Sequence deposited in NCBI GenBank database with the accession number of
ES466900.
