Volume 28, Issue 5
DOI: 10.53555/03276716.2019.01
Computational Prediction and Analysis of Signal Peptide-Bearing TALEs across Xanthomonas oryzae Strains Pathogenic to Rice.
Abstract
Rice (Oryza sativa L.) is a vital food crop for over half of the world's population, with global production reaching approximately 470.63 million metric tonnes. India, the second-largest producer after China, cultivates rice across 42.75 million hectares, achieving an average yield of 3.61 metric tonnes per hectare. However, rice is highly susceptible to diseases caused by fungi, bacteria, viruses, and nematodes, which significantly impact yields. Bacterial leaf blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), can result in yield losses of up to 70%, while bacterial leaf streak, caused by Xanthomonas oryzae pv. oryzicola (Xoc), can lead to losses of 20%.
Transcription activator-like effectors (TALEs) are DNA-binding proteins employed by Xanthomonas bacteria to enhance virulence in host plants by inducing the expression of host susceptibility genes. TALEs are translocated into plant cells via the type III secretion system and possess a central domain with tandem repeats that determine DNA-binding specificity. Each repeat recognises a single base pair, with specific amino acids (RVDs) dictating base recognition. This research investigates the variability of TALEs in different Xanthomonas strains, focusing on Xoo and Xoc. Thirty-four strains were analysed using whole genome sequences obtained from NCBI. Tools such as AnnoTALE, MP3, UniProt, SMS Suite, Clustal X, PSORTb, SignalP, and T346Hunter were utilised for TALE identification, protein prediction, and functional analysis. AnnoTALE identified 592 TALEs across the strains, with further analysis revealing pathogenic proteins, molecular characteristics, and secretion mechanisms.
Examining transcription activator-like effectors (TALEs) in Xanthomonas oryzae has provided valuable insights into how they induce disease in various bacterial types. A total of 592 TALEs were identified from 34 strains, highlighting the genetic diversity of the pathogen. MP3 software predicted that 572 of these proteins are pathogenic, suggesting their involvement in virulence. UniProt analysis identified six homologous protein entries, emphasising their significance in host interactions.
The SMS Suite analysis indicated that the molecular weights of these TALEs range from 80 to 160 kDa, with isoelectric points between 6 and 8, which are crucial for understanding their biochemical properties. Clustal X clustering revealed major protein clusters, indicating conserved sequences that may be critical for their function. PSORTb predictions suggested that most proteins are cytoplasmic, aligning with their role in manipulating host gene expression. Additionally, SignalP identified nine proteins with signal peptides necessary for secretion into host cells, while T346Hunter confirmed the presence of type III secretion systems (T3SS), essential for TALE translocation into host cells. Overall, 310 non-redundant TALEs were identified for further analysis, providing insights into the virulence mechanisms of Xanthomonas species and guiding future strategies to combat rice diseases.
Keywords
Rice (Oryza sativa L.), Transcription Activator-Like Effectors (TALEs), pathogenicity, SignalP server, NCBI Blast.