scholarly journals Dual RNA-Seq Analysis of the Pine-Fusarium circinatum Interaction in Resistant (Pinus tecunumanii) and Susceptible (Pinus patula) Hosts

2019 ◽  
Vol 7 (9) ◽  
pp. 315 ◽  
Author(s):  
Erik A. Visser ◽  
Jill L. Wegrzyn ◽  
Emma T. Steenkamp ◽  
Alexander A. Myburg ◽  
Sanushka Naidoo
Keyword(s):  
Ergosterol Biosynthesis ◽  
Pinus Patula ◽  
Delayed Response ◽  
Fusarium Circinatum ◽  
Rna Seq ◽  
Susceptible Host ◽  
Pinus Tecunumanii ◽  
Host Pathogen ◽  
Phytohormone Signaling ◽  
Pine Species

Fusarium circinatum poses a serious threat to many pine species in both commercial and natural pine forests. Knowledge regarding the molecular basis of pine-F. circinatum host-pathogen interactions could assist efforts to produce more resistant planting stock. This study aimed to identify molecular responses underlying resistance against F. circinatum. A dual RNA-seq approach was used to investigate host and pathogen expression in F. circinatum challenged Pinus tecunumanii (resistant) and Pinus patula (susceptible), at three- and seven-days post inoculation. RNA-seq reads were mapped to combined host-pathogen references for both pine species to identify differentially expressed genes (DEGs). F. circinatum genes expressed during infection showed decreased ergosterol biosynthesis in P. tecunumanii relative to P. patula. For P. tecunumanii, enriched gene ontologies and DEGs indicated roles for auxin-, ethylene-, jasmonate- and salicylate-mediated phytohormone signalling. Correspondingly, key phytohormone signaling components were down-regulated in P. patula. Key F. circinatum ergosterol biosynthesis genes were expressed at lower levels during infection of the resistant relative to the susceptible host. This study further suggests that coordination of phytohormone signaling is required for F. circinatum resistance in P. tecunumanii, while a comparatively delayed response and impaired phytohormone signaling contributes to susceptibility in P. patula.

The tolerance of Pinus patula × Pinus tecunumanii, and other pine hybrids, to Fusarium circinatum in greenhouse trials

New Forests ◽  
2012 ◽  
Vol 44 (3) ◽  
pp. 443-456 ◽  
Author(s):  
R. G. Mitchell ◽  
M. J. Wingfield ◽  
G. R. Hodge ◽  
E. T. Steenkamp ◽  
T. A. Coutinho
Keyword(s):  
Pinus Patula ◽  
Fusarium Circinatum ◽  
Pinus Tecunumanii ◽  
Pine Hybrids

scholarly journals RNA-Sequencing Analyses of Small Bacterial RNAs and their Emergence as Virulence Factors in Host-Pathogen Interactions

2020 ◽  
Vol 21 (5) ◽  
pp. 1627 ◽  
Author(s):  
Idrissa Diallo ◽  
Patrick Provost
Keyword(s):  
Rna Sequencing ◽  
Virulence Factors ◽  
Membrane Vesicles ◽  
Outer Membrane Vesicles ◽  
Rna Seq ◽  
Host Pathogen Interactions ◽  
Bioinformatics Analyses ◽  
Additional Layer ◽  
Host Pathogen

Proteins have long been considered to be the most prominent factors regulating so-called invasive genes involved in host-pathogen interactions. The possible role of small non-coding RNAs (sRNAs), either intracellular, secreted or packaged in outer membrane vesicles (OMVs), remained unclear until recently. The advent of high-throughput RNA-sequencing (RNA-seq) techniques has accelerated sRNA discovery. RNA-seq radically changed the paradigm on bacterial virulence and pathogenicity to the point that sRNAs are emerging as an important, distinct class of virulence factors in both gram-positive and gram-negative bacteria. The potential of OMVs, as protectors and carriers of these functional, gene regulatory sRNAs between cells, has also provided an additional layer of complexity to the dynamic host-pathogen relationship. Using a non-exhaustive approach and through examples, this review aims to discuss the involvement of sRNAs, either free or loaded in OMVs, in the mechanisms of virulence and pathogenicity during bacterial infection. We provide a brief overview of sRNA origin and importance and describe the classical and more recent methods of identification that have enabled their discovery, with an emphasis on the theoretical lower limit of RNA sizes considered for RNA sequencing and bioinformatics analyses.

scholarly journals Hybridization-based capture of pathogen mRNA enables paired host-pathogen transcriptional analysis

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Viktoria Betin ◽  
Cristina Penaranda ◽  
Nirmalya Bandyopadhyay ◽  
Rui Yang ◽  
Angela Abitua ◽  
...  
Keyword(s):  
Transcriptional Profiling ◽  
Transcript Abundance ◽  
Abundant Species ◽  
Single Step ◽  
Sequencing Depth ◽  
Transcriptional Analysis ◽  
Rna Seq ◽  
Low Input ◽  
Temporal Gene Expression ◽  
Host Pathogen

AbstractDual transcriptional profiling of host and bacteria during infection is challenging due to the low abundance of bacterial mRNA. We report Pathogen Hybrid Capture (PatH-Cap), a method to enrich for bacterial mRNA and deplete bacterial rRNA simultaneously from dual RNA-seq libraries using transcriptome-specific probes. By addressing both the differential RNA content of the host relative to the infecting bacterium and the overwhelming abundance of uninformative structural RNAs (rRNA, tRNA) of both species in a single step, this approach enables analysis of very low-input RNA samples. By sequencing libraries before (pre-PatH-Cap) and after (post-PatH-Cap) enrichment, we achieve dual transcriptional profiling of host and bacteria, respectively, from the same sample. Importantly, enrichment preserves relative transcript abundance and increases the number of unique bacterial transcripts per gene in post-PatH-Cap libraries compared to pre-PatH-Cap libraries at the same sequencing depth, thereby decreasing the sequencing depth required to fully capture the transcriptional profile of the infecting bacteria. We demonstrate that PatH-Cap enables the study of low-input samples including single eukaryotic cells infected by 1–3 Pseudomonas aeruginosa bacteria and paired host-pathogen temporal gene expression analysis of Mycobacterium tuberculosis infecting macrophages. PatH-Cap can be applied to the study of a range of pathogens and microbial species, and more generally, to lowly-abundant species in mixed populations.

scholarly journals Next-generation technologies for studying host–pathogen interactions: a focus on dual transcriptomics, CRISPR/Cas9 screening and organs-on-chips

2019 ◽  
Vol 77 (6) ◽  
Author(s):  
Buket Baddal
Keyword(s):  
Infectious Disease ◽  
Drug Targets ◽  
Genome Mining ◽  
Three Dimensional ◽  
Local Environment ◽  
Rna Seq ◽  
Host Pathogen Interactions ◽  
Host Pathogen ◽  
On Chip ◽  
Organ Models

ABSTRACT Pathogens constantly interact with their hosts and the environment, and therefore have evolved unique virulence mechanisms to target and breach host defense barriers and manipulate host immune response to establish an infection. Advances in technologies that allow genome mining, gene editing such as CRISPR/Cas9, genomic, epigenomic and transcriptomic studies such as dual RNA-seq, coupled with bioinformatics, have accelerated the field of host–pathogen interactions within a broad range of infection models. Underpinning of the molecular changes that accompany invasion of eukaryotic cells with pathogenic microorganisms at the intersection of host, pathogen and their local environment has provided a better understanding of infectious disease mechanisms and antimicrobial strategies. The recent evolution of physiologically relevant three-dimensional (3-D) tissue/organ models and microfluidic organ-on-chip devices also provided a window to a more predictive framework of infectious disease processes. These approaches combined hold the potential to highly impact discovery of novel drug targets and vaccine candidates of the future. Here, we review three of the available and emerging technologies—dual RNA-seq, CRISPR/Cas9 screening and organs-on-chips, applicable to the high throughput study and deciphering of interaction networks between pathogens and their hosts that are critical for the development of novel therapeutics.

scholarly journals Resolving host–pathogen interactions by dual RNA-seq

2017 ◽  
Vol 13 (2) ◽  
pp. e1006033 ◽  
Author(s):  
Alexander J. Westermann ◽  
Lars Barquist ◽  
Jörg Vogel
Keyword(s):  
Rna Seq ◽  
Host Pathogen Interactions ◽  
Host Pathogen

Analysis of the wheat andPuccinia triticina (leaf rust) proteomes during a susceptible host-pathogen interaction

PROTEOMICS ◽  
2006 ◽  
Vol 6 (6) ◽  
pp. 1897-1907 ◽  
Author(s):  
Christof Rampitsch ◽  
Natalia V. Bykova ◽  
Brent McCallum ◽  
Eva Beimcik ◽  
Werner Ens
Keyword(s):  
Leaf Rust ◽  
Susceptible Host ◽  
Host Pathogen Interaction ◽  
Host Pathogen

Scanning electron microscopy of Fusarium oxysporum f.sp. lycopersici in xylem vessels of wilt-resistant and susceptible tomato plants

1980 ◽  
Vol 58 (22) ◽  
pp. 2360-2366 ◽  
Author(s):  
Erik L. Stromberg ◽  
Malcolm E. Corden
Keyword(s):  
Electron Microscopy ◽  
Hyphal Growth ◽  
Susceptible Host ◽  
Vessel Elements ◽  
Host Pathogen ◽  
Race 1 ◽  
Perforation Plates ◽  
Susceptible Tomato ◽  
Scanning Electron ◽  
Pathogen Combinations

Vessels in stems of 'Jefferson' (race 1 resistant and race 2 susceptible) and 'Bonny Best' (race 1 and 2 susceptible) tomato cultivars inoculated with Fusarium oxysporum f.sp. lycopersici race 1 or 2 were examined by scanning electron microscopy. Four days after inoculation of Jefferson with conidia of race 1, the inoculum conidia and resultant hyphae generally were collapsed, whereas in the susceptible host–pathogen combinations the inoculum conidia and hyphae appeared normal. Neither the plants of the resistant nor the susceptible host-pathogen combinations had perforation plates or tyloses within vessel elements capable of trapping conidia or effectively blocking hyphal growth. The perforation plates of all vessel elements are reduced to slightly lipped rims and thus provide unrestricted apertures for hyphal growth and conidial movement in the transpiration stream. In the susceptible host–pathogen combinations, mycelial growth often filled the vessels, but no sporulation was noted. Frequent lateral spread of the pathogen occurred between adjacent vessels through the bordered pit-pairs. Infrequent occurrence of tyloses and a lack of occlusions by tyloses in the resistant host–pathogen combination suggest that vascular wilt resistance within the stem is not due primarily to physical containment of the pathogen in the vessels. Collapsed conidia and hyphae in the resistant host–pathogen combination suggests that fungitoxic materials in the vessels suppress the pathogen and contribute to resistance.

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