Atomic Study on Fusarium incarnatum using Bioinformatics tools

¹Madhanraj P.*, ²Ramanathan K., ³Arun N., ⁴Nadimuthu N. and ⁵Panneerselvam A.

¹Department of Microbiology, Thanthai Hans Roever College, Perambalur – 621 212.

²Department of Bioinformatics, Thanthai Hans Roever College, Perambalur – 621 212.

³Department of Biochemistry, Thanthai Hans Roever College, Perambalur – 621 212.

⁴Dept. of Plant Science, Avvaiyar Govt. College for Women, Karaikal – 609 602 Puducherry U.T., India

⁵Department of Botany and Microbiology, A.V.V.M Sri Puspam College, Poondi, Thanjavur – 613 503, Tamil Nadu.

*Corresponding Author E-mail: micromadhan@sify.com

ABSTRACT:

We have been investigating that the atomic study of Fusarium incarnatum with the utilization of Bioinformatics tools. We have been involved in the insilico study on the plant pathogen the Fusarium incarnatum. The involvement of Nucleotides and atoms in this species can be identified with the help of Bioinformatics tools. We can also involved in the analysis of amino acids which are present in this species and calculated the start and stop codons in different frames.

KEY WORDS: Fusarium Incarnatum, Bioinformatics Tools, Nucleotides, Atomic study, Amino acids, Frame Analysis

INTRODUCTION:

Sudden vegetation dieback is the loss of smooth cordgrass along intertidal creeks in salt marshes of the Atlantic and Gulf States. The underlying cause of sudden vegetation dieback remains unclear, but earlier work suggested a contributing role for Fusarium spp. in Louisiana. Fusarium species were associated with S. alterniflora dieback in mid- to north-Atlantic states. Isolations from seven sudden vegetation dieback sites yielded 192 isolates of Fusarium spp., with more than 75% isolated from aboveground tissue. Most isolates fell into two undesirable morphospecies distinguished from each other by macroconidial shape, phialide ontogeny and growth rates. Pathogenicity tests on wound-inoculated S. alterniflora stems and seedling roots revealed that isolates in MS1 were more virulent than those in MS2 but no single isolate caused plant mortality. (Ref 1)

Selenium (Se) is an essential trace element for many organisms including humans, yet toxic at higher levels. Both Se deficiency and toxicity are problems worldwide. Since plants readily accumulate and volatilize Se, they may be used both as a source of dietary Se and for removing excess Se from the environment. Plant species differ in their capacity to metabolize and accumulate Selenium. (Ref 2)

Plant fungal pathogens change their cell wall components during the infection process to avoid degradation by host lytic enzymes, and conversion of the cell wall chitin to chitosan is likely to be one infection strategy of pathogens. Thus, introduction of chitosan-degradation activity into plants is expected to improve fungal disease resistance. Chitosanase has been found in bacteria and fungi, but not in higher plants. (Ref 3)

Eleven reference and 25 clinical isolates of Fusarium were subject to multilocus DNA sequence analysis to determine the species and haplotypes of the fusarial isolates from Beijing and Shandong, China. Seven loci were analyzed: the translation elongation factor 1 alpha gene (EF-1α); the nuclear rRNA internal transcribed spacer (ITS), large subunit (LSU), and intergenic spacer (IGS) regions; the second largest subunit of the RNA polymerase gene (RPB2); the calmodulin gene (CAM); and the mitochondrial small subunit (mtSSU) rRNA gene. (Ref 4)

Laccase production by solid state fermentation) using an indigenously isolated litter dwelling fungus Fusarium incarnatum LD-3 was optimized. Fourteen medium components were screened by the initial screening method of Plackett-Burman. Each of the components was screened on the basis of 'p' probability value which was above 95% confidence level. Ortho-dianisidine, thiamine HCl and CuSO(4). 5 H(2)O were identified as significant components for laccase production. (Ref 5)

Eukaryotic plant pathogens are responsible for the destruction of billions of dollars worth of crops each year. With large-scale genomics of both pathogens and hosts and the corresponding computational analysis, biologists are now able to gain knowledge about many pathogenic and defense genes concurrently. To study the interactions between these two organism groups, it is necessary to design experiments to elucidate the genes being expressed during the invasion of the pathogen into the host. For the most part, this does not require new software development, though it does require the use of existing software in novel ways. (Ref 6)

Species limits within the clinically important Fusarium incarnatum-F. Equiseti and F. chlamydosporum species complexes (FIESC and FCSC, respectively) were investigated using multilocus DNA sequence data. Maximum-parsimony and maximum-likelihood analyses of aligned DNA sequences from four loci resolved 28 species within the FIESC, within which the species were evenly divided among two clades designated incarnatum and Equiseti, and four species within the FCSC. Sequence data from a fifth locus, beta-tubulin, was excluded from the study due to the presence of highly divergent paralogs or xenologs. (Ref 7)

METHODOLOGY:

The Plant Pathogen Fusarium Incarnatum sequence was retrieved from NCBI database and subjected in to PROTOOL for calculating the contribution of Nucleotides in this species. The sequence was also subjected in to Carbana tool for analyzing the composition of atoms in Fusarium Incarnatum. The involvement of amino acids in Fusarium Incarnatum was identified by Protparam tool and this tool also shows the classification of amino acids. The frame analysis can be done by using Translate tool and here we can identify six different frames in the sequence.

RESULTS:

Table 1: Composition of Nucleotides in Fusarium Incarnatum

Atoms	Composition
Adenine	26
Thymine	22
Guanine	23
Cytosine	28

Graph 1: Composition of Nucleotides in Fusarium Incarnatum

Table 2: Composition of Atoms in Fusarium Incarnatum

Atoms	Composition
Carbon	2663
Hydrogen	780
Oxygen	765
Nitrogen	43
Sulphur	4093

Graph 2: Composition of Atoms in Fusarium Incarnatum

DISCUSSION:

The result shows that the composition of nucleotides and atoms in plant pathogen Fusarium Incarnatum. The Table 1 shows that the values for four nucleotides such as Adenine, Guanine, thymine, cytosine and the compositions are 26, 22, 23 and 28 respectively. From the Graph 1, we can easily understand the composition of nucleotides and it shows the contribution of cytosine is very high when compared with other nucleotides. From the table 2, we can able to know about the composition of atoms such as Carbon, Hydrogen, Oxygen, Nitrogen and Sulphur. The composition of carbon is 2663 and the content of Hydrogen is 780. The involvement of oxygen in Fusarium Incarnatum is 765 and nitrogen is 43. The composition value for Sulphur is 4093.The Graph 2 shows that the Geometrical representation of atoms which are involved in this species. From the table 3, we can able to retrieve the position of amino acids which are involved in Fusarium Incarnatum. It shows the number of amino acids is 216. These results were retrieved from Protparam tool. The Table 4, shows that the composition of amino acids in Fusarium Incarnatum. The amino acid Serine which shows that 10.6% and the second highest percentage of amino acid is Arginine (9.7%). It also shows that the positively charged amino acids such as Arginine and Lysine are 27 while the negatively charged amino acids like Aspartic acid and Glutamic acid are 10. The Table 5, which represents that the frames involved in the sequence which are derived from Translate tool. This tool which shows that the start codon and stop codon. The start codon regions are represented by Methionine (ATG). The frames are quoted as 5’3 Frame 1, 5’3 Frame 2, and 5’3 Frame 3 and 3’5 Frame 1, 3’5 Frame 2, and 3’5 Frame 3. Out of these six reading frames, the 3’5 Frame 1 has 5 (ATG) start codons and 4 stop codons.

CONCLUSION:

This study provides the detailed analysis about the plant pathogen Fusarium Incarnatum. When compared with other nucleotides, the contribution of thymine is very low and the cytosine is very high. Regarding with the atomic analysis, the composition of the atom sulphur is very low while the hydrogen is very high. The serine amino acid which shows the value of 10.6% and it belongs to the category Hydrophilic. The derived results from translate tool shows that the start codon and stop codon. From these observations, we concluded that Fusarium Incarnatum which consists of more number of water reflecting amino acids and moderate level of carbon atom. With changes in the nucleotide concentration, amino acid composition and Atom analysis may vary the pathogenicity.

REFERENCES:

1. Elmer WH, Marra RE. New species of Fusarium associated with dieback of Spartina alterniflora in Atlantic salt marshes. Mycologia. 103(4):806-19. (2011)

2. Valdez Barillas JR, Quinn CF, Pilon-Smits EA Selenium accumulation in plants--phytotechnological applications and ecological implications. Int J Phytoremediation.13 (l):166-78. (2011)

3. Kouzai Y, Mochizuki S, Saito A, Ando A, Minami E, Nishizawa Y. Expression of a bacterial chitosanase in rice plants improves disease resistance to the rice blast fungus Magnaporthe oryzae. Plant Cell Rep. 12 (2):145-48. (2011)

4. Wang H, Xiao M, Kong F, Chen S, Dou HT, Sorrell T, Li RY, Xu YC. Accurate and practical identification of 20 Fusarium species by seven-locus sequence analysis and reverse line blot hybridization, and an in vitro antifungal susceptibility study. J Clin Microbial. 49(5):1890-8. (2011)

5. Chhaya U, Gupte A Optimization of media components for laccase production by litter dwelling fungal isolate Fusarium incarnatum LD-3. J Basic Microbiol. 50(1):43-51. (2010)

6. Soderlund C. Brief Bioinform. Computational techniques for elucidating plant-pathogen interactions from large-scale experiments on fungi and oomycetes. 10(6):654-63. (2009)

7. O'Donnell K, Sutton DA, Rinaldi MG, Gueidan C, Crous PW, Geiser DM J Clin Microbiol. Novel multilocus sequence typing scheme reveals high genetic diversity of human pathogenic members of the Fusarium incarnatum-F. Equiseti and .chlamydosporum species complexes within the United States. 47(12):3851-61. (2009)

Received on 17.03.2012 Accepted on 20.04.2012

Asian J. Pharm. Res. 2(2): April-June 2012; Page 78-82