EdeLab & Research Explained!

The sources describe a new database called The Encyclopedia of Domains (TED), which uses deep learning to identify and classify protein domains within the AlphaFold Protein Structure Database (AFDB). TED detects nearly 365 million domains, far exceeding previous methods, and reveals thousands of new folds, superfamily interactions, and domain architectures. TED expands our understanding of structural diversity across the protein universe and provides valuable insights into protein function and evolution.

Source: Exploring structural diversity across the protein universe with The Encyclopedia of Domains

ANDY M. LAU, NICOLA BORDIN , SHAUN M. KANDATHIL , IAN SILLITOE, VAISHALI P. WAMAN, JUDE WELLS, CHRISTINE A. ORENGO, AND DAVID T. JONES

SCIENCE, 1 Nov 2024, Vol 386, Issue 6721, DOI: 10.1126/science.adq4946

This research article examines the potential impact of climate change on Nearctic leafhopper species in North America. The authors utilized species distribution modeling techniques to predict the future distribution and abundance of 14 leafhopper species known to be vectors of phytoplasmas, which are plant pathogens that cause significant economic damage to crops. The study found that the eastern region of North America is currently a hotspot for leafhopper species richness, a trend that is expected to persist under future climate scenarios, with a possible shift towards northern Canada. The analysis revealed that most leafhopper species have similar environmental niches, which could lead to an increase in species overlap and potentially greater transmission of phytoplasma diseases in the future. The authors emphasize the importance of understanding these changes to develop effective pest management strategies for sustainable agriculture.

Source:

Santos, A.A., Jacques, J. & Pérez-López, E. Potential impact of climate change on Nearctic leafhopper distribution and richness in North America. npj Sustain. Agric. 2, 12 (2024). https://doi.org/10.1038/s44264-024-00020-6

This excerpt from the paper "The Plant Immune System" discusses the complex, two-branched defense system plants use against microbial pathogens. The authors describe how plants recognize and respond to pathogen-associated molecular patterns (PAMPs) via pattern recognition receptors (PRRs), which triggers PAMP-triggered immunity (PTI). However, successful pathogens often deploy effectors that interfere with PTI, leading to effector-triggered susceptibility (ETS). The second branch of plant immunity, effector-triggered immunity (ETI), involves the recognition of pathogen effectors by NB-LRR proteins, which often leads to a hypersensitive response (HR) and the arrest of pathogen growth. The paper goes on to examine various mechanisms of host recognition, including both direct and indirect recognition of effectors, and discusses how pathogens evolve to evade host surveillance. It highlights the ongoing co-evolutionary arms race between plants and their pathogens and explores the potential for future research in this field.

This research examines how the plant hormone strigolactone (SL) affects fungal phosphate homeostasis. The study utilizes the model organism Saccharomyces cerevisiae (yeast) to investigate the molecular mechanisms of SL's action. They find that SL inhibits the high-affinity phosphate transporter Pho84 in yeast, leading to phosphate starvation. This mechanism is then confirmed in two plant-associated fungi, Serendipita indica and Fusarium graminearum. The authors suggest that SL may play a role in shaping fungal communities in the rhizosphere and highlight the potential of yeast as a model system for studying plant-fungal interactions.

Source:

Modulation of fungal phosphate homeostasis by the plant hormone strigolactone

James M. Bradley, Michael Bunsick, George Ly, Bruno Aquino, Flora Zhiqi Wang, Duncan Holbrook-Smith, Shingo Suginoo, Dylan Bradizza, Naoki Kato, Omar As’sadiq,1 Nina Marsh, Hiroyuki Osada, François-Didier Boyer, Christopher S.P. McErlean, Yuichiro Tsuchiya, Rajagopal Subramaniam, Dario Bonetta, Peter McCourt, and Shelley Lumba.

https://doi.org/10.1016/j.molcel.2024.09.004

This study presents the assembly and annotation of the full-length mitochondrial genome of the leafhopper species Empoasca fabae. The mitogenome is 14,873 base pairs (bp) long and contains the usual complement of genes for protein-coding, ribosomal RNA, and transfer RNA, as well as a unique D-loop region. Phylogenetic analysis confirmed the placement of E. fabae within the Typhlocybinae subfamily, clustering with other species in the Empoasca genus. The authors conclude that this is the first complete mitochondrial genome for E. fabae from North America, and it will help to further our understanding of the evolutionary relationships within the Empoasca genus and contribute to pest management strategies.

Source: De novo assembly and annotation of the Empoasca fabae mitochondrial genomeJoshua Molligan, Jordanne Jacques, Soham Mukhopadhyay, Edel Perez-Lopez

doi: https://doi.org/10.1101/2024.09.20.614148

This excerpt from Gertrude B. Elion's The Quest for a Cure recounts her remarkable career in medicinal chemistry, particularly her groundbreaking work on purine analogs and their therapeutic applications. The article chronicles her journey from early struggles to find a research position to her leadership in the development of life-saving drugs such as 6-mercaptopurine for leukemia, azathioprine for organ transplantation, allopurinol for gout, and acyclovir for herpes infections. Elion details her key discoveries, the challenges she faced, and the collaborations that enabled her to make these impactful contributions to the field of medicine.

This research article investigates the evolution of effector proteins, secreted proteins that fungal pathogens use to infect plants. The study focuses on sequence-unrelated structurally similar (SUSS) effectors, proteins that share similar structures but have very little sequence similarity, highlighting how these effectors have evolved through divergent evolution and domain fusion. The researchers used AlphaFold2 to predict the structures of 26,653 secreted proteins from 21 fungal species and employed a combination of sequence and structure-based similarity searches to cluster these proteins into families. They found that obligate biotrophs (fungi that depend entirely on their host for survival) exhibited particularly high expansion of SUSS effector families, suggesting unique evolutionary pressures. The study reveals several novel SUSS effector families and suggests that common motifs present in these families likely arose through the extreme expansion and divergence of related proteins, not through independent evolution. This research provides a significant contribution to understanding how fungal pathogens adapt and evolve their effector proteins to overcome plant immunity.

Source: Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses

Kyungyong Seong  & Ksenia V. Krasileva

doi: https://doi.org/10.1038/s41564-022-01287-6

This research paper examines the protein structures of secreted molecules, called effectors, from various gall-forming pathogens, including fungi, oomycetes, and plasmodiophorids. By using AlphaFold2, a powerful machine learning tool for predicting protein structures, the researchers identified several key protein folds that are conserved across kingdoms. The analysis revealed species-specific expansions of certain folds, such as ankyrin repeats in gall-forming plasmodiophorids. Furthermore, the study investigated the evolution of SUSS effector families, which share structural similarity but exhibit extreme sequence divergence. The findings highlight the importance of structure-guided approaches in understanding the diversity of pathogen effectors and their role in manipulating host immunity.

Source:

Structure-guided secretome analysis of gall-forming microbes offers insights into effector diversity and evolution

Soham Mukhopadhyay, Muhammad Asim Javed, Jiaxu Wu, Edel Pérez-López

doi: https://doi.org/10.1101/2024.09.03.609900 https://doi.org/10.7554/eLife.105185.3

This is an excerpt from a review article published in the Annual Review of Plant Biology. The author, David Baulcombe, reflects on his research career which spans over forty years. His research has focused on plant virology, RNA silencing, epigenetics, and plant evolution. Through various anecdotes and examples, the author describes his scientific journey and the importance of having a tractable experimental system to make progress in research. He also touches on the significance of understanding the broader implications of research findings for addressing real-world challenges like food security and plant disease resistance.

Source: Annual Review of Plant Biology

An RNA World

by David C. Baulcombe

Doi: https://doi.org/10.1146/annurev-arplant-070622-021021

This research article focuses on the clubroot pathogen Plasmodiophora brassicae, which is a devastating disease affecting brassica crops worldwide. The authors have successfully sequenced the complete genome of P. brassicae, including the telomeres. This is the first complete genome assembly for any member of the Rhizaria group, to which P. brassicae belongs. The authors annotated the genome, identifying over 10,000 protein-coding genes. This research will be a valuable resource for the plant pathology community as it provides important insights into the evolution, ecology, and pathogenicity of this destructive pathogen.

Full study here:

Telomere-to-telomere Genome Assembly of the Clubroot Pathogen Plasmodiophora Brassicae 

Muhammad Asim Javed, Soham Mukhopadhyay, Eric Normandeau, Anne-Sophie Brochu, Edel Pérez-López

Genome Biology and Evolution, Volume 16, Issue 6, June 2024, evae122, https://doi.org/10.1093/gbe/evae122