Finding the undiscovered roles of genes: an approach using mutual ranking of coexpressed genes and promoter architecture-case study: dual roles of thaumatin like proteins in biotic and abiotic stresses

Regarding the possible multiple functions of a specific gene, finding the alternative roles of genes is a major challenge. Huge amount of available expression data and the central role of the promoter and its regulatory elements provide unique opportunely to address this issue. The question is that how the expression data and promoter analysis can be applied to uncover the different functions of a gene. A computational approach has been presented here by analysis of promoter regulatory elements, coexpressed gene as well as protein domain and prosite analysis. We applied our approach on Thaumatin like protein (TLP) as example. TLP is of group 5 of pathogenesis related proteins which their antifungal role has been proved previously. In contrast, Osmotin like proteins (OLPs) are basic form of TLPs with proved role only in abiotic stresses. We demonstrated the possible outstanding homolouges involving in both biotic and abiotic stresses by analyzing 300 coexpressed genes for each Arabidopsis TLP and OLP in biotic, abiotic, hormone, and light microarray experiments based on mutual ranking. In addition, promoter analysis was employed to detect transcription factor binding sites (TFBs) and their differences between OLPs and TLPs. A specific combination of five TFBs was found in all TLPs presenting the key structure in functional response of TLP to fungal stress. Interestingly, we found the fungal response TFBs in some of salt responsive OLPs, indicating the possible role of OLPs in biotic stresses. Thirteen TFBS were unique for all OLPs and some found in TLPs, proposing the possible role of these TLPs in abiotic stresses. Multivariate analysis showed the possibility of estimating models for distinguishing biotic and abiotic functions of TIPs based on promoter regulatory elements. This is the first report in identifying multiple roles of TLPs and OLPs in biotic and abiotic stresses. This study provides valuable clues for screening and discovering new genes with possible roles in tolerance against both biotic and abiotic stresses. Interestingly, principle component analysis showed that promoter regulatory elements of TLPs and OLPs are more variable than protein properties reinforcing the prominent role of promoter architecture in determining gene function alteration.Tahereh Deihimi, Ali Niazi, Mansour Ebrahimi, Kimia Kajbaf, Somaye Fanaee, Mohammad R. Bakhtiarizadeh and Esmaeile Ebrahimi

Identification and expression analysis of TLPs as candidate genes promoting the responses to both biotic and abiotic stresses in wheat

Thaumatin like protein (TLPs) gene family have the ability to respond to both biotic and abiotic stresses. In this research, gene expression and bioinformatics analysis were applied to reveal the function of TLPs more evidently. Real Time PCR technique was used to compare TLP gene expression between susceptible and resistant cultivars of wheat under the Mycosphaerella graminicola inoculation. Our results indicated the early resistant-related response by TLP up-regulation within 3h after inoculation. In abiotic stress we observed induction of TLP gene expression during salt stress in susceptible cultivar. 50mM NaCl induced rapid induction of TLP within 3h, while 100mM NaCl conferred TLP up-regulation later at 72h. In silico chromosome walking analysis revealed that four loci can be the candidates for conferring tolerance to both biotic and abiotic stresses. In this study, a combination of Real Time PCR technique and bioinformatics tools suggested the possible role of TLP homologs in response to both biotic and abiotic stresses.Tahereh Deihimi, Ali Niazi, Esmaeil Ebrahimiehttp://www.pomics.com/march2013.htm

Bioinformatics and protein engineering; presenting a few applications employed in our labs

Bioinformatics uses various algorithms and methods to explorer huge amount of biological data in order to help us to understand biological mechanisms. In our labs research groups use bioinformatics tools to investigate and understand why some biological processes are working and what are the most important features contributing to their functions. Of special importance to our researchers are some enzymes and proteins responsible for salinity and drought stresses and thermostability. Different approaches have been employed but they can be classified as follows: a. statistical analyses to understand the significant differences among normal and desired proteins (halophilic or thermostable), b. feature selection algorithms to define the most important features contributing to desired protein activities, c. neural network modelings and tools to train and test different networks in order to correlate between features and protein characteristics and use these networks to predict desired abilities. The results of some research groups have been presented briefly here.Mansour Ebrahimi, Esmaeil Ebrahimie, Ahmad Tahmasebi, Narjes Rahpeyma Sarvestani, Tahereh Deihim

Application of neural networks methods to define the most important features contributing to xylanase enzyme thermostability

The importance of finding or making thermostable enzymes in different industries have been highlighted. Therefore, it is inevitable to understand the features involving in enzymes' thermostability. Different approaches have been employed to extract or manufacture thermostable enzymes. Here we have looked at features contributing to Endo-1,4,beta-xylanase (EC 3.2.1.8) thermostability, the key enzyme with possible applications in waste treatment, fuel and chemical production and paper industries. We trained different neural networks with/without feature selection and classification modelling on all available xylanase enzymes amino acids sequences to find features contributing to enzyme thermal stability.M. Ebrahimi, E. Ebrahimie, M. Ebrahimi, T. Deihimi, A. Delavari, M. Mohammadi-dehcheshme

Prédiction de température à court-terme pour horizon de plusieurs heures

International audienceOutside temperature is an important quantity in building control. It enables improvement in inhabitant energy consumption forecast or heating requirement prediction. However most previous works on outside temperature forecasting require either a lot of computation or a lot of different sensors. In this paper we try to forecast outside temperature at a multiple hour horizon knowing only the last 24 hours of temperature and computed clear-sky irradiance up to the prediction horizon. We propose the use different neural networks to predict directly at each hour of the horizon instead of using forecast of one hour to predict the next. We show that the most precise one is using one dimensional convolutions, and that the error is distributed across the year. The biggest error factor we found being unknown cloudiness at the beginning of the day. Our findings suggest that the precision improvement seen is not due to trend accuracy improvement but only due to an improvement in precision

Genome-wide analysis of key salinity-tolerance transporters (HKT1;5) in wheat and wild wheat relatives (A and D genomes)

Exclusion of sodium ions from cells is one of the key salinity tolerance mechanisms in plants. The high-affinity cation transporter (HKT1;5) is located in the plasma membrane of the xylem, excluding Na⁺ from the parenchyma cells to reduce Na⁺ concentration. The regulatory mechanism and exact functions of HKT genes from different genotypic backgrounds are relatively obscure. In this study, the expression patterns of HKT1;5 in A and D genomes of wheat were investigated in root and leaf tissues of wild and domesticated genotypes using real-time PCR. In parallel, the K+/Na⁺ ratio was measured in salt-tolerant and salt-sensitive cultivars. Promoter analysis were applied to shed light on underlying regulatory mechanism of the HKT1;5 expression. Gene isolation and qPCR confirmed the expression of HKT1;5 in the A and D genomes of wheat ancestors (Triticum boeoticum, AbAb and Aegilops crassa, MMDD, respectively). Interestingly, earlier expression of HKT1;5 was detected in leaves compared with roots in response to salt stress. In addition, the salt-tolerant genotypes expressed HKT1;5 before salt-sensitive genotypes. Our results suggest that HKT1;5 expression follows a tissue- and genotype-specific pattern. The highest level of HKT1;5 expression was observed in the leaves of Aegilops, 6 h after being subjected to high salt stress (200 mM). Overall, the D genome allele (HKT1;5-D) showed higher expression than the A genome (HKT1;5-A) allele when subjected to a high NaCl level. We suggest that the D genome is more effective regarding Na⁺ exclusion. Furthermore, in silico promoter analysis showed that TaHKT1;5 genes harbor jasmonic acid response elements.Mahbobeh Zamani Babgohari & Ali Niazi & Ali Asghar Moghadam & Tahereh Deihimi & Esmaeil Ebrahimi