Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing DOI Creative Commons
Annett Erkes, René Grove, Milena Žarković

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Aug. 18, 2022

Abstract Most plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire up to 29 TALE a strain is also referred TALome. DNA-binding domain TALEs comprised highly conserved repeats often occur in gene clusters, precludes the assembly TALE-carrying genomes based on standard sequencing approaches. Here, we report successful 5 Mbp five strains from Oxford Nanopore Technologies (ONT) data. For one these strains, oryzae pv. ( Xoo ) PXO35, illustrate why Illumina short reads longer PacBio are insufficient fully resolve genome. While ONT perfectly suited yield contiguous genomes, they suffer specific error profile within homopolymers. To still complete correct TALomes assemblies, present computational correction pipeline specifically tailored yields at least comparable accuracy Illumina-based polishing. We further systematically assess ONT-based for its multiplexing capacity find that, combined with correction, TALome PXO35 could have been reconstructed less than 20,000 reads. Our results indicate that multiplexed constitutes capable tool characterizing huge collections future.

Language: Английский

The clade III subfamily of OsSWEETs directly suppresses rice immunity by interacting with OsHMGB1 and OsHsp20L DOI Creative Commons
Xin Wang,

Yanhu Ju,

Tao Wu

et al.

Plant Biotechnology Journal, Journal Year: 2024, Volume and Issue: 22(8), P. 2186 - 2200

Published: April 8, 2024

Summary The clade III subfamily of OsSWEETs includes transmembrane proteins necessary for susceptibility to bacterial blight (BB). These genes are targeted by the specific transcription activator‐like effector (TALE) Xanthomonas oryzae pv. and mediate sucrose efflux proliferation. However, mechanism through which regulate rice immunity has not been fully elucidated. Here, we demonstrated that cytosolic carboxyl terminus OsSWEET11a/Xa13 is required complementing PXO99 in IRBB13 ( xa13 / ). Interestingly, C‐terminus ZmXa13, maize homologue OsSWEET11a/Xa13, could perfectly substitute OsSWEET11a/Xa13. Furthermore, interacted with high‐mobility group B1 (OsHMGB1) protein small heat shock‐like OsHsp20L same regions C‐terminus. Consistent physical interactions, knockdown or knockout either OsHMGB1 caused an enhanced PXO99‐resistant phenotype similar OsSWEET11a/OsXa13. Surprisingly, plants was repressed developed increased resistance PXO86, PXO61 YN24, carry TALEs targeting OsSWEET14/Xa41 . Additionally, can interact all six members OsSWEETs, whereas five other addition OsSWEET12. Overall, revealed conserved BB interacting candidates breeding broad‐spectrum disease‐resistant rice.

Language: Английский

Citations

7
Tal6b/AvrXa27A, a hidden TALE targeting the susceptibility gene OsSWEET11a and the resistance gene Xa27 in rice DOI Creative Commons
Zhengyin Xu,

Xiameng Xu,

Ying Li

et al.

Plant Communications, Journal Year: 2023, Volume and Issue: unknown, P. 100721 - 100721

Published: Sept. 1, 2023

Xanthomonas oryzae pv. (Xoo) secretes transcription activator-like effectors (TALEs) to activate rice susceptibility (S), causing bacterial blight (BB), as well resistance (R) genes, leading defense against BB. This activation follows a gene-for-gene paradigm that results in an arms race between the TALE of pathogen and effector-binding elements (EBEs) promoter host genes. In this study, we characterized novel designated Tal6b/AvrXa27A activates S gene OsSWEET11a R Xa27. is member AvrXa27/TalAO class contains 16 repeat variable diresidues (RVDs); Tal6b/AvrXa27A, one RVD altered deleted when compared AvrXa27, known avirulence (avr) effector transcriptionally activated expression both Xa27 via EBEs their corresponding promoters, thus effector-triggered immunity susceptibility, respectively. The RVDs have no obvious similarity with 24 PthXo1, but EBETal6b EBEPthXo1 overlapped promoter. was prevalent among Asian Xoo isolates, PthXo1 has only been reported Philippine strain PXO99A. Genome editing further corroborated requirement for Tal6b/AvrXa27A-dependent Xoo. Moreover, resulted higher than OsSWEET11a, which led strong, rapid response blocked disease development. These findings suggest plays dual functions: triggering by activating factor while inducing resulting virulence. Intriguingly, Tal6b/AvrXa27A,but not can bind OsSWEET11a. underlying recognition mechanism remains unclear appears deviate from currently accepted TALE-DNA code.

Language: Английский

Citations

14
Exploring the shared pathogenic strategies of independently evolved effectors across distinct plant viruses DOI
Lulu Li, Jianping Chen, Zongtao Sun

et al.

Trends in Microbiology, Journal Year: 2024, Volume and Issue: 32(10), P. 1021 - 1033

Published: March 22, 2024

Language: Английский

Citations

5
Genome Editing of Plant Mitochondrial and Chloroplast Genomes DOI Creative Commons
Shin‐ichi Arimura, Issei Nakazato

Plant and Cell Physiology, Journal Year: 2023, Volume and Issue: 65(4), P. 477 - 483

Published: Dec. 19, 2023

Abstract Plastids (including chloroplasts) and mitochondria are remnants of endosymbiotic bacteria, yet they maintain their own genomes, which encode vital components for photosynthesis respiration, respectively. Organellar genomes have distinctive features, such as being present multicopies, mostly inherited maternally, having characteristic genomic structures undergoing frequent homologous recombination. To date, it has proven to be challenging modify these genomes. For example, while CRISPR/Cas9 is a widely used system editing nuclear genes, not been successfully applied organellar Recently, however, precise gene-editing technologies Protein-based enzymes, especially transcription activator–like effector nucleases (TALENs) artificial enzymes utilizing DNA-binding domains TALENs (TALEs), by harnessing organellar-targeting signals. This short review introduces discusses the use targeted base editors in effects potential applications plant science breeding.

Language: Английский

Citations

11
Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing DOI Creative Commons
Annett Erkes, René Grove, Milena Žarković

et al.

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: March 27, 2023

Most plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire up to 29 TALE a strain is also referred TALome. DNA-binding domain TALEs comprised highly conserved repeats often occur in gene clusters, precludes the assembly TALE-carrying genomes based on standard sequencing approaches.Here, we report successful 5 Mbp five strains from Oxford Nanopore Technologies (ONT) data. For one these strains, oryzae pv. (Xoo) PXO35, illustrate why Illumina short reads longer PacBio are insufficient fully resolve genome. While ONT perfectly suited yield contiguous genomes, they suffer specific error profile within homopolymers. To still complete correct TALomes assemblies, present computational correction pipeline specifically tailored yields at least comparable accuracy Illumina-based polishing. We further systematically assess ONT-based for its multiplexing capacity find that, combined with correction, TALome Xoo PXO35 could have been reconstructed less than 20,000 reads.Our results indicate that multiplexed constitutes capable tool characterizing huge collections future.

Language: Английский

Citations

10
Sugar transporters: mediators of carbon flow between plants and microbes DOI Creative Commons
Ming Lei,

Xiaodi Wang,

Kuan Chen

et al.

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 16

Published: April 16, 2025

Pathogens and symbiotic microorganisms significantly influence plant growth crop productivity. Enhancing disease resistance maximizing the beneficial role of in agriculture constitute critical areas scientific investigation. A fundamental aspect plant-microorganisms interactions revolves around nutritional dynamics, characterized by either "food shortage" or supply" scenarios. Notably, pathogenic predominantly utilize photosynthetic sugars as their primary carbon source during host colonization. This phenomenon has generated substantial interest regulatory mechanisms governing sugar transport redistribution at plant-microorganism interface. Sugar transporters, which primarily mediate allocation to various sink organs, have emerged crucial players plant-pathogen establishment associations. review systematically categorized transporters highlighted functional significance mediating with microorganisms. Furthermore, we synthesized recent advancements understanding molecular these identified key questions warranting further Elucidating roles offers novel strategies for enhancing health productivity, thereby contributing agricultural sustainability global food security.

Language: Английский

Citations

0
Bacteria suppress immune responses in Arabidopsis by inducing methylglyoxal accumulation and promoting H2O2 scavenging DOI
Tingting Yuan,

Yu-Rui Feng,

Cheng Hua

et al.

Developmental Cell, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

Citations

0
Recent advances in innovative strategies for plant disease resistance breeding DOI Creative Commons
Dekun Wang, Rong Yang, Mengting Liu

et al.

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 16

Published: May 21, 2025

Plant disease poses a great threat to crop production. The mechanisms underlying plant-pathogen interactions are critical research topics worldwide. In recent years, significant breakthrough studies have been reported, broadening our understanding of plant immunity. Based on these findings, many strategies developed improve defense against various diseases. Here, we summarize and their applications in aimed at promoting resistance. Besides domain swapping, gene shuffling, random mutation, three additional the last decade. first strategy is editing host susceptibility ( S ) genes prevent pathogen infection. Editing Mlo DMR6 species good examples this approach. second promoters or resistance R genes. This widely used counteract Xanthomonas , such as modifying LOB1 SWEET several crops enhance third designing products, especially nucleotide-binding leucine-rich repeat (NLR) receptors. approach based growing knowledge structural features NLRs, which seen advances recently. To date, all NLR-engineering attempts focused rice paired Pikp-1/Pikp-2 (allelic Pikm-1/Pikm-2) RGA4/RGA5. bioengineering NLRs provides promising method combat diverse pathogens. Detailed also discussed review, organized around strategies. summary, with progresses immune mechanism, innovative molecular available mitigate pathogens future.

Language: Английский

Citations

0
Recent Progress in Rice–Xanthomonas oryzae Interactions DOI Creative Commons

Yuting Qi,

Qiong Rao,

Chenglong Lu

et al.

Biology, Journal Year: 2025, Volume and Issue: 14(5), P. 471 - 471

Published: April 25, 2025

Rice bacterial blight (BB) and leaf streak (BLS), caused by Xanthomonas oryzae pv. (Xoo) oryzicola (Xoc), respectively, are among the most devastating diseases threatening global rice production. The interactions between complex dynamic, involving recognition, attack, defense, adaptation mechanisms enacted both host pathogens. This review summarizes recent advances in understanding rice–Xanthomonas interactions, focusing on infection models, pathogenic mechanisms, immune responses elicited oryzae. Special attention is devoted to roles of transcription activator-like effectors (TALEs) non-TALE pathogenicity, functions resistance (R) genes interconnected molecular networks derived from multi-omics approaches. Understanding these essential for developing effective disease-resistance strategies creating elite disease-resistant varieties.

Language: Английский

Citations

0
Plant NLRs: Evolving with pathogen effectors and engineerable to improve resistance DOI Creative Commons
Biaoming Zhang,

Mengting Liu,

Yanchao Wang

et al.

Frontiers in Microbiology, Journal Year: 2022, Volume and Issue: 13

Published: Sept. 28, 2022

Pathogens are important threats to many plants throughout their lifetimes. Plants have developed different strategies overcome them. In the plant immunity system, nucleotide-binding domain and leucine-rich repeat-containing proteins (NLRs) most common components. And recent studies greatly expanded our understanding of how NLRs function in plants. this review, we summarize on mechanism processes effector recognition, resistosome formation, defense activation. Typical divided into three groups according domains at N termini interrelated ways immunity. Atypical contain additional integrated (IDs), some which directly interact with pathogen effectors. Plant evolve effectors exhibit specific recognition. Meanwhile, been successfully engineered confer resistance new pathogens based accumulated studies. summary, pioneering obtained NLR researches, though more questions arise as a result huge number NLRs. However, broadened mechanism, will be components for engineering improvement.

Language: Английский

Citations

13