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Review
. 2019 Aug 17;7(8):269.
doi: 10.3390/microorganisms7080269.

Exploration of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era

Rahul Mahadev Shelake  1 , Dibyajyoti Pramanik  1 , Jae-Yean Kim  2   3
Affiliations
Review

Exploration of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era

Rahul Mahadev Shelake et al. Microorganisms. .

Abstract

Plants and microbes are co-evolved and interact with each other in nature. Plant-associated microbes, often referred to as plant microbiota, are an integral part of plant life. Depending on the health effects on hosts, plant-microbe (PM) interactions are either beneficial or harmful. The role of microbiota in plant growth promotion (PGP) and protection against various stresses is well known. Recently, our knowledge of community composition of plant microbiome and significant driving factors have significantly improved. So, the use of plant microbiome is a reliable approach for a next green revolution and to meet the global food demand in sustainable and eco-friendly agriculture. An application of the multifaceted PM interactions needs the use of novel tools to know critical genetic and molecular aspects. Recently discovered clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) tools are of great interest to explore PM interactions. A systematic understanding of the PM interactions will enable the application of GE tools to enhance the capacity of microbes or plants for agronomic trait improvement. This review focuses on applying GE techniques in plants or associated microbiota for discovering the fundamentals of the PM interactions, disease resistance, PGP activity, and future implications in agriculture.

Keywords: CRISPR/Cas; genome editing; plant disease resistance; plant growth promotion; plant microbiome.

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Conflict of interest statement

The authors declare no conflict of interest that might be perceived as affecting the objectivity of this review.

Figures

Figure 1
Figure 1
Microbiome in plant ecosystem. Schematic plant and plant-associated microbiota colonizing different niches on and inside the plant tissue. All the above-ground plant parts together, called the phyllosphere, are a continuously evolving habitat due to ultraviolet (UV) radiation and altering climatic conditions. It is primarily composed of leaves. Below-ground plant parts, mainly roots, are generally influenced by soil properties. Harmful interactions affect the plant growth through pathogenic activities of some microbiota members (left side). On the other hand, beneficial microbial interactions promote plant growth (right side).
Figure 2
Figure 2
Driving factors of plant–microbe interactions. Environment-, soil- and plant-mediated factors determine the composition and structure of host microbiota. Furthermore, plant–plant, microbe–microbe, and plant–microbe interactions also impact the plant and soil microbiome.
Figure 3
Figure 3
Biology and components of site-specific nucleases (SSNs) modified for genome editing applications. (A) Repair of double-strand breaks (DSBs) in damaged DNA strands occurs through two main pathways that consist of non-homologous end-joining (NHEJ) and homology-directed repair (HDR). NHEJ is most common in cells. It is an error-prone pathway that introduces indel mutations (small insertions or deletions). HDR is more precise compared to NHEJ, but it requires a donor template that results in either insertion or replacement. (B) Zinc finger nuclease (ZNF) is designed using an array of DNA-binding domains from zinc-finger proteins. Each ZFN comprises DNA-binding domain at N-terminus and FokI nuclease at C-terminus. The linker and spacers are shown in black and pink, respectively. (C) Design of transcription activator-like effectors (TALE) protein-based nuclease (TALEN) bound to DNA. (D) Illustration of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 with a sgRNA (red) encoding gRNA (green) bound to a target DNA (blue) adjacent to PAM, i.e., protospacer adjacent motif (magenta). Cleavage sites on both strands shown with scissors and dotted line depict the blunt ends produced by Cas9. (E) CRISPR/Cpf1 (Cas12a) system shown with a crRNA (red), a gRNA (green), target DNA (blue), PAM (magenta). Cleavage sites of both strands (scissors) produce staggered ends (dotted line) with Cpf1.
Figure 4
Figure 4
Schematic representation of Cas9 and Cpf1 variants including domain organization. Color scheme and nomenclature to represent domains followed from published structures for each enzyme. MbCpf1 structure is not yet available, hence protein domains are not drawn. Abbreviations: RuvCI-III, RuvC nuclease domain; Arg, arginine-rich bridge helix; REC1-3, recognition lobe; HNH, HNH-like nuclease domain; CTD, C-terminal domain; WEDI-III, wedge domain; PI, PAM-interacting domain; BH, bridge helix; Nuc, novel nuclease domain; OBD, oligonucleotide-binding domain; LHD, looped-out helical domain; HLH, helix-loop-helix; UK, domain with unknown functions.
Figure 5
Figure 5
Expanding CRISPR toolkit, including applications beyond genome editing, are shown. The CRISPR-based tools have been designed for various applications in diverse fields. The SpCas9-mediated knock-out or knock-in strategy is most widely implemented in prokaryotes and eukaryotes. Catalytically dead Cas9 (dCas9) or nickase Cas9 (nCas9) and Cas9 orthologs fused with specific modulators have been reprogrammed to perform base editing (ABE, adenine base editor; CBE, cytidine base editor) RNA editing, screening libraries, chromatin imaging, transcription regulation, allele generation using the EvolvR system, and epigenome editing. Further details of each technique discussed in the main text.
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