scholarly journals The Manganese Peroxidase Gene Family of Trametes trogii: Gene Identification and Expression Patterns Using Various Metal Ions under Different Culture Conditions

2021 ◽  
Vol 9 (12) ◽  
pp. 2595
Author(s):  
Yu Zhang ◽  
Zhongqi Dong ◽  
Yuan Luo ◽  
En Yang ◽  
Huini Xu ◽  
...  
Keyword(s):  
Metal Ions ◽  
Gene Family ◽  
Liquid Culture ◽  
Extracellular Enzymes ◽  
Expression Patterns ◽  
White Rot Fungi ◽  
Culture Conditions ◽  
White Rot ◽  
Type I ◽  
Group I

Manganese peroxidases (MnPs), gene family members of white-rot fungi, are necessary extracellular enzymes that degrade lignocellulose and xenobiotic aromatic pollutants. However, very little is known about the diversity and expression patterns of the MnP gene family in white-rot fungi, especially in contrast to laccases. Here, the gene and protein sequences of eight unique MnP genes of T. trogii S0301 were characterized. Based on the characteristics of gene sequence, all TtMnPs here belong to short-type hybrid MnP (type I) with an average protein length of 363 amino acids, 5–6 introns, and the presence of conserved cysteine residues. Furthermore, analysis of MnP activity showed that metal ions (Mn2+ and Cu2+) and static liquid culture significantly influenced MnP activity. A maximum MnP activity (>14.0 U/mL) toward 2,6-DMP was observed in static liquid culture after the addition of Mn2+ (1 mM) or Cu2+ (0.2 or 2 mM). Moreover, qPCR analysis showed that Mn2+ obviously upregulated the Group I MnP subfamily (T_trogii_09901, 09904, 09903, and 09906), while Cu2+ and H2O2, along with changing temperatures, mainly induced the Group II MnP subfamily (T_trogii_11984, 11971, 11985, and 11983), suggesting diverse functions of fungal MnPs in growth and development, stress response, etc. Our studies here systematically analyzed the gene structure, expression, and regulation of the TtMnP gene family in T. trogii, one of the important lignocellulose-degrading fungi, and these results extended our understanding of the diversity of the MnP gene family and helped to improve MnP production and appilications of Trametes strains and other white-rot fungi.

Genome-wide identification and analysis of the MADS-box gene family and its potential role in fruit ripening in black raspberry (Rubus occidentalis L.)

2021 ◽  
pp. 1-15
Author(s):  
Yaqiong Wu ◽  
Chunhong Zhang ◽  
Wenlong Wu ◽  
Weilin Li ◽  
Lianfei Lyu
Keyword(s):  
Gene Family ◽  
Fruit Ripening ◽  
Fruit Development ◽  
Expression Patterns ◽  
Type I ◽  
Black Raspberry ◽  
Mads Box ◽  
Mads Box Genes ◽  
Genome Wide ◽  
Mads Box Gene

BACKGROUND: Black raspberry is a vital fruit crop with a high antioxidant function. MADS-box genes play an important role in the regulation of fruit development in angiosperms. OBJECTIVE: To understand the regulatory role of the MADS-box family, a total of 80 MADS-box genes were identified and analyzed. METHODS: The MADS-box genes in the black raspberry genome were analyzed using bioinformatics methods. Through an analysis of the promoter elements, the possible functions of different members of the family were predicted. The spatiotemporal expression patterns of members of the MADS-box family during black raspberry fruit development and ripening were systematically analyzed. RESULTS: The genes were classified into type I (Mα: 33; Mβ: 6; Mγ: 10) and type II (MIKC *: 2; MIKCC: 29) genes. We also obtained a complete overview of the RoMADS-box gene family through phylogenetic, gene structure, conserved motif, and cis element analyses. The relative expression analysis showed different expression patterns, and most RoMADS-box genes were more highly expressed in fruit than in other tissues of black raspberry. CONCLUSIONS: This finding indicates that the MADS-box gene family is involved in the regulation of fruit ripening processes in black raspberry.

scholarly journals A Novel Approach in Crude Enzyme Laccase Production and Application in Emerging Contaminant Bioremediation

Processes ◽  
2020 ◽  
Vol 8 (6) ◽  
pp. 648
Author(s):  
Luong N. Nguyen ◽  
Minh T. Vu ◽  
Md Abu Hasan Johir ◽  
Nirenkumar Pathak ◽  
Jakub Zdarta ◽  
...  
Keyword(s):  
Steroid Hormones ◽  
Liquid Culture ◽  
Emerging Contaminants ◽  
White Rot Fungi ◽  
Enzyme Concentration ◽  
Crude Enzyme ◽  
White Rot ◽  
Laccase Production ◽  
Solid Culture ◽  
Novel Approach

Laccase enzyme from white-rot fungi is a potential biocatalyst for the oxidation of emerging contaminants (ECs), such as pesticides, pharmaceuticals and steroid hormones. This study aims to develop a three-step platform to treat ECs: (i) enzyme production, (ii) enzyme concentration and (iii) enzyme application. In the first step, solid culture and liquid culture were compared. The solid culture produced significantly more laccase than the liquid culture (447 vs. 74 µM/min after eight days), demonstrating that white rot fungi thrived on a solid medium. In the second step, the enzyme was concentrated 6.6 times using an ultrafiltration (UF) process, resulting in laccase activity of 2980 µM/min. No enzymatic loss due to filtration and membrane adsorption was observed, suggesting the feasibility of the UF membrane for enzyme concentration. In the third step, concentrated crude enzyme was applied in an enzymatic membrane reactor (EMR) to remove a diverse set of ECs (31 compounds in six groups). The EMR effectively removed of steroid hormones, phytoestrogen, ultraviolet (UV) filters and industrial chemical (above 90%). However, it had low removal of pesticides and pharmaceuticals.

scholarly journals Comparison of the Decay Behavior of Two White-Rot Fungi in Relation to Wood Type and Exposure Conditions

2020 ◽  
Vol 8 (12) ◽  
pp. 1931
Author(s):  
Ehsan Bari ◽  
Geoffrey Daniel ◽  
Nural Yilgor ◽  
Jong Sik Kim ◽  
Mohammad Ali Tajick-Ghanbary ◽  
...  
Keyword(s):  
Cell Wall ◽  
Moisture Content ◽  
Wood Species ◽  
White Rot Fungi ◽  
White Rot ◽  
High Mass ◽  
Type I ◽  
Oak Wood ◽  
Mass Losses ◽  
Decay Behavior

Fungal wood decay strategies are influenced by several factors, such as wood species, moisture content, and temperature. This study aims to evaluate wood degradation characteristics of spruce, beech, and oak after exposure to the white-rot fungi Pleurotusostreatus and Trametesversicolor. Both fungi caused high mass losses in beech wood, while spruce and oak wood were more resistant to decay. The moisture content values of the decayed wood correlated with the mass losses for all three wood species and incubation periods. Combined microscopic and chemical studies indicated that the two fungi differed in their decay behavior. While T. versicolor produced a decay pattern (cell wall erosion) typical of white-rot fungi in all wood species, P. ostreatus caused cell wall erosion in spruce and beech and soft-rot type I (cavity formation) decay in oak wood. These observations suggest that P. ostreatus may have the capacity to produce a wider range of enzymes/radicals triggered by the chemical composition of wood cell walls and/or local compositional variability within the cell wall.

PCB’s Biotransformation by a White-Rot Fungus Under Composting and Liquid Culture Conditions

2002 ◽  
pp. 287-297
Author(s):  
G. Ruiz-Aguilar ◽  
J. Fernández-Sánchez ◽  
R. Rodríguez-Vázquez ◽  
H. M. Poggi-Varaldo ◽  
F. Esparza-García ◽  
...  
Keyword(s):  
Liquid Culture ◽  
Culture Conditions ◽  
White Rot ◽  
White Rot Fungus

Extracellular Enzymes of the White Rot Fungi

2001 ◽  
Vol 3 (2-3) ◽  
pp. 1
Author(s):  
Cristina N. Dumitrache-Anghel ◽  
Danielle Tilmanis ◽  
Lyndal Roberts ◽  
Warren L. Baker ◽  
Greg T. Lonergan
Keyword(s):  
Extracellular Enzymes ◽  
White Rot Fungi ◽  
White Rot

scholarly journals Gene Expression Patterns of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium Are Influenced by Wood Substrate Composition during Degradation

2016 ◽  
Vol 82 (14) ◽  
pp. 4387-4400 ◽  
Author(s):  
Oleksandr Skyba ◽  
Dan Cullen ◽  
Carl J. Douglas ◽  
Shawn D. Mansfield
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
White Rot Fungi ◽  
Wood Decay ◽  
White Rot ◽  
Decay Fungi ◽  
Content Type ◽  
Postia Placenta ◽  
Substrate Composition ◽  
Wood Decay Fungi

ABSTRACTIdentification of the specific genes and enzymes involved in the fungal degradation of lignocellulosic biomass derived from feedstocks with various compositions is essential to the development of improved bioenergy processes. In order to elucidate the effect of substrate composition on gene expression in wood-rotting fungi, we employed microarrays based on the annotated genomes of the brown- and white-rot fungi,Rhodonia placenta(formerlyPostia placenta) andPhanerochaete chrysosporium, respectively. We monitored the expression of genes involved in the enzymatic deconstruction of the cell walls of three 4-year-oldPopulus trichocarpa(poplar) trees of genotypes with distinct cell wall chemistries, selected from a population of several hundred trees grown in a common garden. The woody substrates were incubated with wood decay fungi for 10, 20, and 30 days. An analysis of transcript abundance in all pairwise comparisons highlighted 64 and 84 differentially expressed genes (>2-fold,P< 0.05) inP. chrysosporiumandP. placenta, respectively. Cross-fungal comparisons also revealed an array of highly differentially expressed genes (>4-fold,P< 0.01) across different substrates and time points. These results clearly demonstrate that gene expression profiles ofP. chrysosporiumandP. placentaare influenced by wood substrate composition and the duration of incubation. Many of the significantly expressed genes encode “proteins of unknown function,” and determining their role in lignocellulose degradation presents opportunities and challenges for future research.IMPORTANCEThis study describes the variation in expression patterns of two wood-degrading fungi (brown- and white-rot fungi) during colonization and incubation on three different naturally occurring poplar substrates of differing chemical compositions, over time. The results clearly show that the two fungi respond differentially to their substrates and that several known and, more interestingly, currently unknown genes are highly misregulated in response to various substrate compositions. These findings highlight the need to characterize several unknown proteins for catalytic function but also as potential candidate proteins to improve the efficiency of enzymatic cocktails to degrade lignocellulosic substrates in industrial applications, such as in a biochemically based bioenergy platform.

scholarly journals Comparative study on laccase activity of white rot fungi under submerged fermentation with different lignocellulosic wastes

BioResources ◽  
2020 ◽  
Vol 15 (4) ◽  
pp. 9166-9179
Author(s):  
Qi An ◽  
Jie Qiao ◽  
Lu-Sen Bian ◽  
Mei-Ling Han ◽  
Xun-You Yan ◽  
...  
Keyword(s):  
Submerged Fermentation ◽  
Laccase Activity ◽  
White Rot Fungi ◽  
Industrial Applications ◽  
Culture Conditions ◽  
White Rot ◽  
Laccase Production ◽  
Poplar Wood ◽  
Lignocellulosic Wastes ◽  
Cottonseed Hull

Different Pleurotus ostreatus and Flammulina velutipes species were compared relative to their ability to produce laccase in submerged fermentation of various lignocellulosic wastes. Fungi cultivation in identical culture conditions revealed wide differences among both species and strains of the same species. The laccase secretion ability of P. ostreatus strains was superior to F. velutipes strains. Maximum laccase production on cottonseed hull, corncob, and poplar wood was secreted by P. ostreatus CY 568, P. ostreatus CCEF 89, and P. ostreatus CY 568, respectively. The nature of lignocellulosic materials played an important role in determining the expression of laccase potential of fungi. The presence of cottonseed hull improved laccase activity and accelerated the rate of enzyme production. Maximum laccase production on cottonseed hull was nearly 1.29-fold and 1.53-fold higher than that on corncob and poplar wood, respectively. Laccase activity was detected in almost all tested strains on cottonseed hull on the first day, while only a few strains on poplar wood and corncob were detected on the first day. These findings will be helpful for selecting the appropriate strain in industrial applications and for optimization of integrated industrial laccase production.

scholarly journals Genome-wide identification and analyses of the AHL gene family in cotton (Gossypium)

2019 ◽  
Author(s):  
Lanjie Zhao ◽  
Youjun Lu ◽  
Wei Chen ◽  
Jinbo Yao ◽  
Yan Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Orthologous Gene ◽  
Potential Functions ◽  
Pcr Analysis ◽  
Type I ◽  
Clade B ◽  
Genome Wide

Abstract Background: Members of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED ( AHL ) family are involved in various plant biological processes via protein-DNA and protein-protein interaction. However, no the systematic identification and analysis of AHL gene family have been reported in cotton. Results: To investigate the potential functions of AHLs in cotton, genome-wide identification, expressions and structure analysis of the AHL gene family were performed in this study. 48, 51 and 99 AHL genes were identified from the G.raimondii, G.arboreum and G.hirsutum genome, respectively. Phylogenetic analysis revealed that the AHLs in cotton evolved into 2 clades, Clade-A with 4-5 introns and Clade-B with intronless (excluding AHL 20-2). Based on the composition of the AT-hook motif(s) and PPC/DUF 296 domain, AHL proteins were classified into three types (Type-I/-II/-III), with Type-I AHLs forming Clade-B, and the other two types together diversifying in Clade-A. The detection of synteny and collinearity showed that the AHLs expanded with the WGD in cotton, and the sequence structure of AHL20-2 showed the tendency of increasing intron in three different Gossypium spp . The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates of orthologous gene pairs revealed that the AHL genes of G.hirsutum had undergone through various selection pressures, purifying selection mainly in A-subgenome and positive selection mainly in D-subgenome. Examination of their expression patterns showed most of AHLs of Clade-B expressed predominantly in stem, while those of Clade-A in ovules, suggesting that the AHLs within each clade shared similar expression patterns with each other. qRT-PCR analysis further confirmed that some GhAHLs higher expression in stems and ovules. Conclusion: In this study, 48, 51 and 99 AHL genes were identified from three cotton genomes respectively. AHLs in cotton were classified into two clades by phylogenetic relationship and three type based on the composition of motif and domain. The AHLs expanded with segmental duplication, not tandem duplication. The expression profiles of GhAHLs revealed abundant differences in expression levels in various tissues and at different stages of ovules development. Our study provided significant insights into the potential functions of AHLs in regulating the growth and development in cotton.

scholarly journals Comparison of the Ability of Several White-rot Fungi to Biobleach Acacia Oxygen-delignified Kraft Pulp

2019 ◽  
pp. 1-10
Author(s):  
Sitompul Afrida ◽  
Toshihiro Watanabe ◽  
Yutaka Tamai
Keyword(s):  
Kraft Pulp ◽  
Extracellular Enzymes ◽  
Low Cost ◽  
White Rot Fungi ◽  
Acacia Mangium ◽  
White Rot ◽  
Irpex Lacteus ◽  
Lentinus Tigrinus

Previous screening analyses demonstrated that the in vivo biobleaching activities of the white-rot fungi Irpex lacteus KB-1.1 and Lentinus tigrinus LP-7 are higher than those of Phanerochaete chrysosporium and Trametes versicolor. The purpose of the current study was to examine the production of extracellular enzymes of these four white-rot fungi grown on three types of low-cost media containing agricultural and forestry waste, and to evaluate the ability of the produced extracellular enzymes to biobleach Acacia oxygen-delignified kraft pulp (A-OKP). The biobleaching activity of extracellular fractions of I. lacteus, L. tigrinus, T. versicolor, and P. chrysosporium cultures was the most pronounced after 3 days of incubation with Acacia mangium wood powder supplemented with rice bran and 1% glucose (WRBG) with resultant Kappa number reduction of 4.4%, 6.7%, 3.3%, and 3.3%, respectively. Therefore, biobleaching ability of I. lacteus and L. tigrinus have been shown to be higher than of T. versicolor and P. chrysosporium, both in vivo and in vitro.

scholarly journals Molecular Evolution of the Vacuolar Iron Transporter (VIT) Family Genes in 14 Plant Species

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 144 ◽  
Author(s):  
Jun Cao
Keyword(s):  
Gene Family ◽  
Plant Species ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Gene Organization ◽  
Development Stages ◽  
Functional Studies ◽  
Iron Transporter ◽  
Group I ◽  
Conserved Gene

The vacuolar iron transporter (VIT) proteins are involved in the storage and transport of iron. However, the evolution of this gene family in plants is unknown. In this study, I first identified 114 VIT genes in 14 plant species and classified these genes into seven groups by phylogenetic analysis. Conserved gene organization and motif distribution implied conserved function in each group. I also found that tandem duplication, segmental duplication and transposition contributed to the expansion of this gene family. Additionally, several positive selection sites were identified. Divergent expression patterns of soybean VIT genes were further investigated in different development stages and under iron stress. Functional network analysis exhibited 211 physical or functional interactions. The results will provide the basis for further functional studies of the VIT genes in plants.

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