Computational identification, homology modelling and docking analysis of phytase protein from Fusarium oxysporum

AbstractThe extracellular phytase structural gene was isolated from phytopathogenic fungus Fusarium oxysporum using PCR amplification (GenBank accession number KC708486). The gene possesses an open reading frame of 1,514 bp and two coding regions 1–44 and 156–1458 with one intron (45–155). The phy gene from F. oxysporum (Fophy) encodes a putative phytase protein of F. oxysporum (FoPhy) of 448 amino acids, which includes a putative signal peptide (21 residues). The deduced amino acid sequence of FoPhy exhibits 98% sequence identity with Aspergillus niger and Aspergillus awamori phytases. The deduced protein sequence contains the consensus motifs (RHGXRXP and HD), eight conserved cysteine residues and ten conserved putative N-glycosylation sites, which are conserved among histidine acid phosphatases. Computed structural model of FoPhy was found to consist of mixed α/β motifs and probable loops. The predicted model resembles the structure of Aspergillus niger phytase (root mean square deviation 0.23 Å). Ramachandran plot analysis revealed that 95.0% portion of residues fall into the most favourable regions. The predicted three-dimensional structures of FoPhy on molecular docking with substrates like inositol hexaphosphate, inositol hexasulphate and N-acetyl D-glucosamine showed its interaction with conserved histidine and aspartic acid residues in the active site, as also known for other fungal phytases. This study provides a detailed identification and characterization of the phytase from F. oxysporum, which may be helpful in elucidation of its role in pathogenesis and other transcriptional and expression studies.

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Substrate (aglycone) specificity of human cytosolic beta-glucosidase

Biochemical Journal ◽

10.1042/bj20021876 ◽

2003 ◽

Vol 373 (1) ◽

pp. 41-48 ◽

Cited By ~ 55

Author(s):

Jean-Guy BERRIN ◽

Mirjam CZJZEK ◽

Paul A. KROON ◽

W. Russell MCLAUCHLAN ◽

Antoine PUIGSERVER ◽

...

Keyword(s):

Structural Model ◽

Homology Modelling ◽

Three Dimensional ◽

Amino Acid Residues ◽

Dimensional Model ◽

Three Dimensional Model ◽

Mutant Proteins ◽

Metabolizing Enzyme ◽

Beta Glucosidase

Human cytosolic β-glucosidase (hCBG) is a xenobiotic-metabolizing enzyme that hydrolyses certain flavonoid glucosides, with specificity depending on the aglycone moiety, the type of sugar and the linkage between them. Based upon the X-ray structure of Zea mays β-glucosidase, we generated a three-dimensional model of hCBG by homology modelling. The enzyme exhibited the (β/α)8-barrel fold characteristic of family 1 β-glucosidases, with structural differences being confined mainly to loop regions. Based on the substrate specificity of the human enzymes, sequence alignment of family 1 enzymes and analysis of the hCBG structural model, we selected and mutated putative substrate (aglycone) binding site residues. Four single mutants (Val168→Tyr, Phe225→Ser, Tyr308→Ala and Tyr308→Phe) were expressed in Pichia pastoris, purified and characterized. All mutant proteins showed a decrease in activity towards a broad range of substrates. The Val168→Tyr mutation did not affect Km on p-nitrophenyl (pNP)-glycosides, but increased Km 5-fold on flavonoid glucosides, providing the first biochemical evidence supporting a role for this residue in aglycone-binding of the substrate, a finding consistent with our three-dimensional model. The Phe225→Ser and Tyr308→Ala mutations, and, to a lesser degree, the Tyr308→Phe mutation, resulted in a drastic decrease in specific activities towards all substrates tested, indicating an important role of those residues in catalysis. Taken together with the three-dimensional model, these mutation studies identified the amino-acid residues in the aglycone-binding subsite of hCBG that are essential for flavonoid glucoside binding and catalysis.

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Complete Genome Sequence of a Novel Mitovirus From the Phytopathogenic Fungus Fusarium Oxysporum

10.21203/rs.3.rs-416498/v1 ◽

2021 ◽

Author(s):

Jing wang ◽

Rui Qiu ◽

Chengjun Li ◽

Shujun Li ◽

Xiaojie Li ◽

...

Keyword(s):

Fusarium Oxysporum ◽

Root Rot ◽

Sequence Similarity ◽

Distinct Species ◽

Phytopathogenic Fungus ◽

Limited Information ◽

Reading Frame ◽

Rdrp Domain ◽

Mitochondrial Genetic Code ◽

The Family

Abstract Fusarium oxysporum is a cosmopolitan plant pathogen causing Fusarium wilt and Fusarium root rot in many economically important crops. There is still limited information about mycoviruses that infect F. oxysporum. Here, a novel mitovirus tentatively named Fusarium oxysporum mitovirus 1 (FoMV1) was identified from F. oxysporum strain B2-10. The genome of FoMV1 is 2,453 nt in length with a predicted AU content of 71.6%, and contains one large open reading frame (ORF) using the fungal mitochondrial genetic code. The ORF encodes RNA-dependent RNA polymerases (RdRp) of 723 amino acids with a molecular mass of 84.98 kDa. The RdRp domain of FoMV1 shares 29.01–68.43% sequence similarity to the members of the family Mitoviridae. Phylogenetic analysis further suggested that FoMV1 is a new member of a distinct species in the genus Mitovirus.

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Population genetic variation analysis of bitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae in China using inter simple sequence repeats (ISSR) molecular markers

Journal of Plant Pathology ◽

10.1007/s42161-021-00759-8 ◽

2021 ◽

Author(s):

Rui Zang ◽

Ying Zhao ◽

Kangdi Guo ◽

Kunqi Hong ◽

Huijun Xi ◽

...

Keyword(s):

Genetic Variation ◽

Genetic Differentiation ◽

Fusarium Oxysporum ◽

Diversity Index ◽

Gene Diversity ◽

Pcr Amplification ◽

Bitter Gourd ◽

Diseased Plant ◽

Variation Analysis ◽

Group I

AbstractBitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae (FOM) is a devastating crop disease in China. A total of 173 isolates characteristic of typical Fusarium oxysporum with abundant microconidia and macroconidia on white or ruby colonies were obtained from diseased plant tissues. BLASTn analysis of the rDNA-ITS of the isolates showed 99% identity with F. oxysporum species. Among the tested isolates, three were infectious toward tower gourd and five were pathogenic to bottle gourd. However, all of the isolates were pathogenic to bitter gourd. For genetic differences analysis, 40 ISSR primers were screened and 11 primers were used for ISSR-PCR amplification. In total, 127 loci were detected, of which 76 were polymorphic at a rate of 59.84%. POPGENE analysis showed that Nei’s gene diversity index (H) and Shannon’s information index (I) were 0.09 and 0.15, respectively, which indicated that the genetic diversity of the 173 isolates was low. The coefficient of gene differentiation (Gst = 0.33 > 0.15) indicated that genetic differentiation was mainly among populations. The strength of gene flow (Nm = 1.01 > 1.0) was weak, indicating that the population differentiation caused by gene drift was blocked to some degree. The dendrogram based on ISSR markers showed that the nine geographical populations were clustered into two groups at the threshold of genetic similarity coefficient of 0.96. The Shandong and Henan populations were clustered into Group I, while the Guangdong, Hainan, Guangxi, Fujian, Jiangxi, and Hubei populations constituted Group II. Results of the genetic variation analysis showed that the Hunan and Guangxi populations had the highest degree of genetic differentiation, while the Hubei population had the lowest genetic differentiation. Our findings enrich the knowledge of the genetic variation characteristics of FOM populations with the goal of developing effective disease-management programs and resistance breeding programs.

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Na3Co2(As0.52P0.48)O4(As0.95P0.05)2O7

Acta Crystallographica Section E Structure Reports Online ◽

10.1107/s1600536813032029 ◽

2013 ◽

Vol 69 (12) ◽

pp. i85-i86 ◽

Cited By ~ 1

Author(s):

Youssef Ben Smida ◽

Abderrahmen Guesmi ◽

Mohamed Faouzi Zid ◽

Ahmed Driss

Keyword(s):

Solid State ◽

Solid State Reaction ◽

Title Compound ◽

General Position ◽

Structural Model ◽

Three Dimensional ◽

The Other ◽

Coordination Polyhedra ◽

Bond Valence Sum ◽

Full Occupancy

The title compound, trisodium dicobalt(II) (arsenate/phosphate) (diarsenate/diphosphate), was prepared by a solid-state reaction. It is isostructural with Na3Co2AsO4As2O7. The framework shows the presence of CoX22O12(X2 is statistically disordered with As0.95P0.05) units formed by sharing corners between Co1O6octahedra andX22O7groups. These units form layers perpendicular to [010]. Co2O6octahedra andX1O4(X1 = As0.54P0.46) tetrahedra form Co2X1O8chains parallel to [001]. Cohesion between layers and chains is ensured by theX22O7groups, giving rise to a three-dimensional framework with broad tunnels, running along thea- andc-axis directions, in which the Na+ions reside. The two Co2+cations, theX1 site and three of the seven O atoms lie on special positions, with site symmetries 2 andmfor the Co,mfor theX1, and 2 andm(× 2) for the O sites. One of two Na atoms is disordered over three special positions [occupancy ratios 0.877 (10):0.110 (13):0.066 (9)] and the other is in a general position with full occupancy. A comparison between structures such as K2CdP2O7, α-NaTiP2O7and K2MoO2P2O7is made. The proposed structural model is supported by charge-distribution (CHARDI) analysis and bond-valence-sum (BVS) calculations. The distortion of the coordination polyhedra is analyzed by means of the effective coordination number.

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Complete Genome Sequence of a Novel Ourmia-like Mycovirus Infecting the Phytopathogenic Fungus Botryosphaeria Dothidea

10.21203/rs.3.rs-505029/v1 ◽

2021 ◽

Author(s):

Liying Sun ◽

Ziqian Lian ◽

Subha Das ◽

Jingxian Luo ◽

Ida Bagus Andika

Keyword(s):

Amino Acid ◽

Genome Sequence ◽

Amino Acid Sequences ◽

Shanxi Province ◽

Phytopathogenic Fungus ◽

Botryosphaeria Dothidea ◽

Reading Frame ◽

Ring Rot ◽

Ssrna Virus ◽

The Family

Abstract In this study, we describe the full-length genome sequence of a novel ourmia-like mycovirus, tentatively designated Botryosphaeria dothidea ourmia-like virus 1 (BdOLV1), isolated from the phytopathogenic fungus, Botryosphaeria dothidea strain P8, associated with apple ring rot in Shanxi province, China. The complete BdOLV1 genome is comprised of 2797 nucleotides, a positive-sense (+) single-stranded RNA (ssRNA) with a single open reading frame (ORF). The ORF putatively encodes a 642-amino acid polypeptide with conserved RNA-dependent RNA polymerase (RdRp) motifs, related to viruses of the family Botourmiaviridae. Phylogenetic analysis based on the RdRp amino acid sequences showed that BdOLV1 is grouped with oomycete-infecting unclassified viruses closely related to the genus Botoulivirus in Botourmiaviridae. This is the first report of a novel (+)ssRNA virus in B. dothidea related to the genus Botoulivirus in the family Botourmiaviridae.

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Genetica e produção de amiloglicosidase em Aspergillus awamori e no hibrido interespecifico com Aspergillus niger

10.47749/t/unicamp.1987.52766 ◽

1987 ◽

Author(s):

Airton Vialta

Keyword(s):

Aspergillus Niger ◽

Aspergillus Awamori

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Qualidade sanitária e fisiológica de sementes de abóbora variedade Menina Brasileira

Fitopatologia Brasileira ◽

10.1590/s0100-41582006000200006 ◽

2006 ◽

Vol 31 (2) ◽

pp. 158-163 ◽

Cited By ~ 4

Author(s):

Derblai Casaroli ◽

Danton C. Garcia ◽

Marlove F. B. Muniz ◽

Nilson L. de Menezes

Keyword(s):

Aspergillus Niger ◽

Fusarium Oxysporum ◽

Alternaria Alternata ◽

Penicillium Digitatum ◽

Cucurbita Moschata ◽

Rhizopus Stolonifer ◽

Cladosporium Cucumerinum

O trabalho teve como objetivos avaliar e correlacionar a qualidade sanitária e fisiológica de sementes de abóbora, variedade Menina Brasileira (Cucurbita moschata.). Foram avaliados dois lotes de sementes de abóbora produzidas no sistema agroecológico e quatro no sistema convencional, com e sem tratamento químico. Os lotes foram submetidos aos testes de sanidade, seguindo a metodologia do "Blotter test", com congelamento, germinação e vigor (primeira contagem, índice de velocidade de germinação, envelhecimento acelerado e emergência de plântulas). Os resultados indicaram a separação dos lotes de diferentes origens a partir da qualidade sanitária e fisiológica, onde as maiores incidências de fungos foram observadas nos lotes agroecológicos e o maior potencial fisiológico foi observado nos lotes de origem convencional não tratados. Foram encontrados os fungos Fusarium oxysporum, Alternaria alternata, Cladosporium cucumerinum, Aspergillus niger, Penicillium digitatum, Rhizopus stolonifer e Phoma terrestris. A qualidade sanitária não interferiu na qualidade fisiológica das sementes de abóbora, variedade Menina Brasileira.

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Analysis of The Open Reading Frame (ORF) 29-TrnC (GCA) Sequence to Detect Indica and Japonica Sub Species on Upland Rice of Situ Bagendit and Inbred Rice of Ciherang

Biosaintifika Journal of Biology & Biology Education ◽

10.15294/biosaintifika.v10i1.12626 ◽

2018 ◽

Vol 10 (1) ◽

pp. 153-159

Author(s):

Rohma Istiana ◽

Hermin Pancasakti Kusumaningrum ◽

Rejeki Siti Ferniah

Keyword(s):

Plant Breeding ◽

Upland Rice ◽

Pcr Amplification ◽

Breeding Program ◽

Abiotic Factor ◽

Reading Frame ◽

Plant Breeding Program ◽

Pcr Products

The identification and the characterization of genetic diversity of rice was the first step in the rice plant breeding program. This study aimed to detect indica or japonica sub-species on upland rice Situ Bagendit and inbred rice Ciherang using molecular markers ORF 29-TrnC (GCA) on the chloroplast genome. Rice was included to the indica sub-species if the 32 bp insertion on ORF 29-TrnC (GCA) sequence was found, on the contrary, if the deletion 32 bp on ORF 29-TrnC (GCA) was found then it was included to the japonica sub-species. DNA isolation was examined from the leaves of the rice plants, and then it tested quantitatively to determine the transparency and DNA concentration from the isolation results. PCR amplification was performed using a pair of primers CP2 and it was followed by agarose gel electrophoresis. The visualization of the DNA bands used the gel documentation. Sequencing of PCR products produced a long base 390 bp in Situ Bagendit rice and 390 bp in Ciherang rice. Analysis of the sequences showed that the insertions occurred throughout the 32 bp in Situ Bagendit rice and the insertions occurred throughout the 32 bp in Ciherang rice. The results showed that upland rice Situ Bagendit and inbred rice Ciherang were included in the indica sub-species. The knowledge of variety of genetics of rice can be used as bio-information in the plant breeding program. Further, the knowledge can be used to protect in genetic power source, the selection and the composing of superior varieties of rice which is tolerant with kinds of biotic and abiotic factor.

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