4.7 Article

Genome-wide identification of the class III peroxidase gene family of sugarcane and its expression profiles under stresses

Related references

Note: Only part of the references are listed.
Article Biotechnology & Applied Microbiology

Genome-wide characterization and functional analysis of class III peroxidase gene family in soybean reveal regulatory roles of GsPOD40 in drought tolerance

Muqadas Aleem et al.

Summary: This study provides a comprehensive report on the characterization of the GmPOD gene family in soybean, including gene number, distribution, classification, and evolutionary mechanisms. Differential expression of some GmPODs between drought-tolerant and drought-sensitive genotypes was observed, with GsPOD40 enhancing drought tolerance in soybean by regulating defense response pathways.

GENOMICS (2022)

Article Biotechnology & Applied Microbiology

SignalP 6.0 predicts all five types of signal peptides using protein language models

Felix Teufel et al.

Summary: Signal peptides are short amino acid sequences that regulate protein secretion and translocation. SignalP 6.0, a machine learning model, is introduced to detect all types of signal peptides, including those applicable to metagenomic data.

NATURE BIOTECHNOLOGY (2022)

Article Plant Sciences

The IbBBX24-IbTOE3-IbPRX17 module enhances abiotic stress tolerance by scavenging reactive oxygen species in sweet potato

Huan Zhang et al.

Summary: The study revealed that the transcription factor IbBBX24 regulates the expression of peroxidase gene IbPRX17, enhancing sweet potato tolerance to salt and drought stresses. Overexpression lines of IbBBX24 and IbPRX17 showed higher peroxidase activity and lower H2O2 accumulation under abiotic stress conditions. Additionally, the interaction between IbBBX24 and APETALA2 protein IbTOE3 was found to improve the response to abiotic stress in sweet potato and tobacco plants.

NEW PHYTOLOGIST (2022)

Article Biochemistry & Molecular Biology

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Andrew D. Yates et al.

Summary: Ensembl Genomes provides access to non-vertebrate genomes complementing the vertebrate resources developed by the Ensembl project, creating one of the most comprehensive genomic resources globally. They are focused on reducing genome redundancy and improving gene annotation, pangenome analysis, data dissemination speed, and support for the microbial research community.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

TimeTree 5: An Expanded Resource for Species Divergence Times

Sudhir Kumar et al.

Summary: The fifth edition of the TimeTree of Life resource (TToL5) synthesizes published molecular timetrees to make evolutionary knowledge easily accessible. It contains divergence time information on 137,306 species, an increase of 41% from the previous edition. The web interface is now ADA-compliant and mobile-friendly.

MOLECULAR BIOLOGY AND EVOLUTION (2022)

Article Plant Sciences

The class III peroxidase gene family is involved in ascorbic acid induced delay of internal browning in pineapple

Xiaowan Hou et al.

Summary: Excessive production of ROS can be toxic to organisms, but the PRXs class of peroxidases in plants play a crucial role in maintaining ROS homeostasis. In this study, pineapples were soaked in ascorbic acid to reduce ROS and PPO activity, which successfully restrained the spread of internal browning (IB). With the identification of 78 pineapple PRX genes, research revealed their potential role in negatively regulating IB occurrence. This research provides valuable insights for further understanding the molecular mechanisms of IB and developing IB-resistant pineapple varieties.

FRONTIERS IN PLANT SCIENCE (2022)

Article Multidisciplinary Sciences

Genome-wide identification and functional analysis of class III peroxidases in Gossypium hirsutum

Yi Chen et al.

Summary: In this study, the Class III peroxidase (PRX) gene family in cotton was identified, classified, and analyzed for evolution. The GhPRX107 gene was found to play a crucial role in pollen fertility, regulating the levels of reactive oxygen species (ROS) in anthers.

PEERJ (2022)

Article Genetics & Heredity

Genome-Wide Identification and Analysis of the Class III Peroxidase Gene Family in Tobacco (Nicotiana tabacum)

Lingtong Cheng et al.

Summary: This study conducted a comprehensive analysis of the peroxidase (POD) gene family in tobacco and identified 210 non-redundant members. These genes were unevenly distributed throughout the 24 tobacco chromosomes and clustered into six subgroups based on phylogenetic analysis. Gene structure and motif analyses revealed the structural and functional diversity among the subgroups. The study also suggested that the evolution of NtPOD genes is influenced by segmental duplication and purifying selection. The expression patterns of NtPODs in different tissues and under various stress treatments were investigated, showing tissue-specific expression patterns and potential involvement in biotic and abiotic responses. qRT-PCR analyses and fluorescence assays confirmed the expression patterns and plasma membrane localization of NtPOD genes. Overall, these findings provide valuable insights into the evolution and function of the tobacco POD gene family.

FRONTIERS IN GENETICS (2022)

Article Biochemistry & Molecular Biology

The Class III peroxidase gene OsPrx30, transcriptionally modulated by the AT-hook protein OsATH1, mediates rice bacterial blight-induced ROS accumulation

Hao Liu et al.

Summary: The study revealed the important role of OsPrx30 in rice immunity against Xanthomonas oryzae pv. oryzae, showing that overexpression of OsPrx30 increases susceptibility to the pathogen. Furthermore, transcription of OsPrx30 is regulated by the AT-hook transcription factor OsATH1, and depletion of OsATH1 results in increased susceptibility to the pathogen.

JOURNAL OF INTEGRATIVE PLANT BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Comparative Analysis of Sugar Metabolites and Their Transporters in Sugarcane Following Sugarcane mosaic virus (SCMV) Infection

Sehrish Akbar et al.

Summary: Through transcriptome and proteomics analysis, this study revealed that the Badila sugarcane genotype showed significant upregulation of sugar metabolizing and transporting transcripts after infection with Sugarcane mosaic virus (SCMV), potentially enhancing virus multiplication and infection.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Plant Sciences

Functional analysis of four Class III peroxidases from Chinese pear fruit: a critical role in lignin polymerization

Xi Zhu et al.

Summary: In this study, five PRXs were cloned from Chinese pear and found to play critical roles in lignin biosynthesis. The enzyme activity and subcellular localization of these PRXs varied, with PbPRX2 shown to be important for polymerization of lignin in pear fruit. The results suggest that PbPRXs are key in lignin biosynthesis in Chinese pear fruit.

PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS (2021)

Article Virology

Sugarcane mosaic virus remodels multiple intracellular organelles to form genomic RNA replication sites

Jipeng Xie et al.

Summary: Positive-stranded RNA viruses like potyviruses remodel host endomembrane system to form virus-induced intracellular vesicles for replication. Different potyviruses infect different host plants with potential differences in infection mechanisms.

ARCHIVES OF VIROLOGY (2021)

Article Biochemistry & Molecular Biology

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

Ivica Letunic et al.

Summary: The Interactive Tree Of Life is an online tool for displaying, manipulating, and annotating phylogenetic and other trees. The latest version 5 introduces a new tree display engine and several new features, such as a new dataset type and expanded annotation options. Users can now also manually annotate trees by hand, providing more flexibility and control.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

Pfam: The protein families database in 2021

Jaina Mistry et al.

Summary: The Pfam database has recently added a large number of protein families and domains, made revisions for COVID-19 research, and introduced Pfam-B as a supplement. These updates and improvements can help researchers classify protein sequences more effectively and conduct related studies.

NUCLEIC ACIDS RESEARCH (2021)

Review Biochemistry & Molecular Biology

Progress in our understanding of plant responses to the stress of heavy metal cadmium

Tingting Zhu et al.

Summary: Heavy metal pollution, especially cadmium, negatively affects plant growth and development by inhibiting processes such as seed germination, photosynthesis, and antioxidation. Extensive research has been conducted on the toxic effects of Cd2+ on plants and the mechanisms of Cd(2+) tolerance.

PLANT SIGNALING & BEHAVIOR (2021)

Article Biochemistry & Molecular Biology

CDD/SPARCLE: the conserved domain database in 2020

Shennan Lu et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemistry & Molecular Biology

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

Chengjie Chen et al.

MOLECULAR PLANT (2020)

Review Biochemical Research Methods

Lignin biosynthesis and its integration into metabolism

Ruben Vanholme et al.

CURRENT OPINION IN BIOTECHNOLOGY (2019)

Article Biochemistry & Molecular Biology

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Multidisciplinary Sciences

A mosaic monoploid reference sequence for the highly complex genome of sugarcane

Olivier Garsmeur et al.

NATURE COMMUNICATIONS (2018)

Article Genetics & Heredity

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Jisen Zhang et al.

NATURE GENETICS (2018)

Article Plant Sciences

Field Performance of Transgenic Sugarcane Lines Resistantto Sugarcane Mosaic Virus

Wei Yao et al.

FRONTIERS IN PLANT SCIENCE (2017)

Review Plant Sciences

Diverse functions and reactions of class III peroxidases

Jun Shigeto et al.

NEW PHYTOLOGIST (2016)

Review Biochemistry & Molecular Biology

Roles of cell wall peroxidases in plant development

Edith Francoz et al.

PHYTOCHEMISTRY (2015)

Article Biochemical Research Methods

GSDS 2.0: an upgraded gene feature visualization server

Bo Hu et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

Yupeng Wang et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Plant Sciences

Enzymatic activity and proteomic profile of class III peroxidases during sugarcane stem development

Igor Cesarino et al.

PLANT PHYSIOLOGY AND BIOCHEMISTRY (2012)

Article Multidisciplinary Sciences

Characterizing the role of rice NRAMP5 in Manganese, Iron and Cadmium Transport

Yasuhiro Ishimaru et al.

SCIENTIFIC REPORTS (2012)

Review Biochemistry & Molecular Biology

Evolution of structure and function of Class I peroxidases

Marcel Zamocky et al.

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS (2010)

Article Biochemistry & Molecular Biology

Circos: An information aesthetic for comparative genomics

Martin Krzywinski et al.

GENOME RESEARCH (2009)

Article Biochemistry & Molecular Biology

Phylogenetic relationships in class I of the superfamily of bacterial, fungal, and plant peroxidases

M Zámocky

EUROPEAN JOURNAL OF BIOCHEMISTRY (2004)

Article Biochemistry & Molecular Biology

The class III peroxidase multigenic in land plants family in rice and its evolution

F Passardi et al.

PHYTOCHEMISTRY (2004)

Article Biochemistry & Molecular Biology

Lignin peroxidase structure and function

K Piontek et al.

BIOCHEMICAL SOCIETY TRANSACTIONS (2001)