Genome-Wide Identification and Expression Analysis of the ALKB Homolog Gene Family in Potato ( L.).

Int J Mol Sci

Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China.

Published: October 2024

AI Article Synopsis

  • The study investigates the role of 11 AlkB homolog (ALKBH) genes related to mA methylation in potato, focusing on their functions in RNA metabolism and plant development.
  • Researchers conducted a comprehensive analysis of these genes’ characteristics, evolutionary relationships, and expression patterns across different potato tissues, finding high expression in stolon and flower parts.
  • Results indicate that most ALKBH genes are responsive to phytohormones and abiotic stress (excluding cold), paving the way for future research on mA methylation mechanisms in potatoes.

Article Abstract

-methyladenosine (mA) is an abundant and pervasive post-transcriptional modification in eukaryotic mRNAs. AlkB homolog (ALKBH) proteins play crucial roles in RNA metabolism and translation, participating in mA methylation modification to regulate plant development. However, no comprehensive investigations have been conducted on in potato. Here, 11 family genes were identified in potato and renamed according to BLASTP and phylogenetic analyses following the genome. The characteristics, sequence structures, motif compositions, phylogenetics, chromosomal locations, synteny, and promoter -acting element predictions were analyzed, revealing distinct evolutionary relationships between potato and other species (tomato and ). Homologous proteins were classified into seven groups depending on similar conserved domains, which implies that they possess a potentially comparable function. Moreover, the s were ubiquitous, and their expression was examined in the various tissues of a whole potato, in which the genes, except for were most highly expressed in the stolon and flower. Multiple hormone and stress-response elements were found to be located in the promoters of the genes. Further qRT-PCR results suggest that they may be significantly upregulated in response to phytohormones and abiotic stress (except for cold), and the expression of most of the genes exhibited positively modulated trends. Overall, this study is the first to report a genome-wide assessment of the family in potato, providing valuable insights into candidate gene selection and facilitating in-depth functional analyses of ALKBH-mediated mA methylation mechanisms in potato.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11507222PMC
http://dx.doi.org/10.3390/ijms252010984DOI Listing

Publication Analysis

Top Keywords

alkb homolog
8
family potato
8
potato
7
genome-wide identification
4
identification expression
4
expression analysis
4
analysis alkb
4
homolog gene
4
gene family
4
potato -methyladenosine
4

Similar Publications

Decoding the mA epitranscriptomic landscape for biotechnological applications using a direct RNA sequencing approach.

Nat Commun

January 2025

National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.

Epitranscriptomic modifications, particularly N6-methyladenosine (mA), are crucial regulators of gene expression, influencing processes such as RNA stability, splicing, and translation. Traditional computational methods for detecting mA from Nanopore direct RNA sequencing (DRS) data are constrained by their reliance on experimentally validated labels, often resulting in the underestimation of modification sites. Here, we introduce pum6a, an innovative attention-based framework that integrates positive and unlabeled multi-instance learning (MIL) to address the challenges of incomplete labeling and missing read-level annotations.

View Article and Find Full Text PDF

ALKBH5 suppresses gastric cancer tumorigenesis and metastasis by inhibiting the translation of uncapped WRAP53 RNA isoforms in an m6A-dependent manner.

Mol Cancer

January 2025

Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, No. 651 Dongfeng Road East, Guangzhou, 510060, People's Republic of China.

The N6-methyladenosine (m6A) modification serves as an essential epigenetic regulator in eukaryotic cells, playing a significant role in tumorigenesis and cancer progression. However, the detailed biological functions and underlying mechanisms of m6A regulation in gastric cancer (GC) are poorly understood. Our research revealed that the m6A demethylase ALKBH5 was markedly downregulated in GC tissues, which was associated with poor patient prognosis.

View Article and Find Full Text PDF

RNA mA involves in regulation of oxidative stress and apoptosis may via NF-kB pathway in cadmium-induced lung cells.

Cell Death Discov

January 2025

Institute of Preventive Medicine, School of Public Health, Dali University, No. 22, Wanhua Road, Dali, Yunnan, 671000, PR China.

Cadmium has been identified as an environmental pollutant and a carcinogen. N-methyladenosine (mA) plays a crucial role in the development of lung tumors, but the mechanisms remain incompletely clarified. In present study, our data demonstrated that prolonged treatment of 1 μmol/L CdSO for 40 passages in bronchial epithelial cells (Beas-2B cells) resulted in the development of a malignant phenotype, which manifested as boosted proliferation, migration and invasion capacity as well as apoptosis reduction.

View Article and Find Full Text PDF

The significance of ALKBH5 in erasing mRNA methylation in mRNA biogenesis, decay, and translation control has emerged as a prominent research focus. Additionally, ALKBH5 is associated with the development of numerous human cancers. However, it remains unclear whether ALKBH5 regulates the growth and metastasis of papillary thyroid carcinoma (PTC).

View Article and Find Full Text PDF

ALKBH5 facilitates tumor progression via an m6A-YTHDC1-dependent mechanism in glioma.

Cancer Lett

January 2025

Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282 China. Electronic address:

N-methyladenosine (m6A) methylation, is a well-known epigenetic modification involved in various biological processes, including tumorigenesis. However, the role of AlkB homolog 5 (ALKBH5), a critical component of m6A modification, remains unclear in glioma. This study investigates the function of ALKBH5 in glioma progression and its potential as a therapeutic target.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!