skip to main content


Title: Multiplexed CRISPR/Cas9 editing of the long‐chain acyl‐CoA synthetase family in the diatom Phaeodactylum tricornutum reveals that mitochondrial ptACSL3 is involved in the synthesis of storage lipids
Summary

Long‐chain acyl‐CoA synthetases (LACS) play diverse and fundamentally important roles in lipid metabolism. While their functions have been well established in bacteria, yeast and plants, the mechanisms by which LACS isozymes regulate lipid metabolism in unicellular oil‐producing microalgae, including the diatomPhaeodactylum tricornutum, remain largely unknown.

InP. tricornutum, a family of five genes (ptACSL1ptACSL5) encodes LACS activities. We generated singlelacsknockout/knockdown mutants using multiplexed CRISPR/Cas9 method, and determined their substrate specificities towards different fatty acids (FAs) and subcellular localisations.

ptACSL3 is localised in the mitochondria and its disruption led to compromised growth and reduced triacylglycerol (TAG) content when cells were bubbled with air. TheptACSL3mutants showed altered FA profiles in two galactoglycerolipids and phosphatidylcholine (PC) with significantly reduced distribution of 16:0 and 16:1. ptACSL5 is localised in the peroxisome and its knockdown resulted in reduced growth rate and altered molecular species of PC and TAG, indicating a role in controlling the composition of acyl‐CoAs for lipid synthesis.

Our work demonstrates the potential of generating gene knockout mutants with the mutation of large fragment deletion using multiplexed CRISPR/Cas9 and provides insight into the functions of LACS isozymes in lipid metabolism in the oleaginous microalgae.

 
more » « less
NSF-PAR ID:
10370620
Author(s) / Creator(s):
 ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  
Publisher / Repository:
Wiley-Blackwell
Date Published:
Journal Name:
New Phytologist
Volume:
233
Issue:
4
ISSN:
0028-646X
Page Range / eLocation ID:
p. 1797-1812
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. SUMMARY

    Genetic compensation has been proposed to explain phenotypic differences between gene knockouts and knockdowns in several metazoan and plant model systems. With the rapid development of reverse genetic tools such as CRISPR/Cas9 and RNAi in microalgae, it is increasingly important to assess whether genetic compensation affects the phenotype of engineered algal mutants. While exploring triacylglycerol (TAG) biosynthesis pathways in the model algaChlamydomonas reinhardtii, it was discovered that knockout of certain genes catalyzing rate‐limiting steps of TAG biosynthesis, type‐2 diacylglycerol acyltransferase genes (DGTTs), triggered genetic compensation under abiotic stress conditions. Genetic compensation of aDGTT1null mutation by a relatedPDATgene was observed regardless of the strain background or mutagenesis approach, for example, CRISPR/Cas 9 or insertional mutagenesis. However, no compensation was found in thePDATknockout mutant. The effect ofPDATknockout was evaluated in a Δvtc1mutant, in whichPDATwas upregulated under stress, resulting in a 90% increase in TAG content. Knockout ofPDATin the Δvtc1background induced a 12.8‐fold upregulation ofDGTT1and a 272.3% increase in TAG content in Δvtc1/pdat1cells, while remaining viable. These data suggest that genetic compensation contributes to the genetic robustness of microalgal TAG biosynthetic pathways, maintaining lipid and redox homeostasis in the knockout mutants under abiotic stress. This work demonstrates examples of genetic compensation in microalgae, implies the physiological relevance of genetic compensation in TAG biosynthesis under stress, and provides guidance for future genetic engineering and mutant characterization efforts.

     
    more » « less
  2. Summary

    In seed plants, 1‐aminocyclopropane‐1‐carboxylic acid (ACC) is the precursor of the plant hormone ethylene but also has ethylene‐independent signaling roles. Nonseed plants produce ACC but do not efficiently convert it to ethylene. InArabidopsis thaliana, ACC is transported by amino acid transporters, LYSINE HISTIDINE TRANSPORTER 1 (LHT1) and LHT2. In nonseed plants,LHThomologs have been uncharacterized.

    Here, we isolated an ACC‐insensitive mutant (Mpain) that is defective in ACC uptake in the liverwortMarchantia polymorpha. Mpaincontained a frameshift mutation (1 bp deletion) in the MpLHT1coding sequence, and was complemented by expression of a wild‐type MpLHT1transgene. Additionally, ACC insensitivity was re‐created in CRISPR/Cas9‐Mplht1knockout mutants. We found that MpLHT1 can also transportl‐hydroxyproline andl‐histidine.

    We examined the physiological functions of MpLHT1in vegetative growth and reproduction based on mutant phenotypes. Mpainand Mplht1plants were smaller and developed fewer gemmae cups compared to wild‐type plants. Mplht1mutants also had reduced fertility, and archegoniophores displayed early senescence.

    These findings reveal that MpLHT1 serves as an ACC and amino acid transporter inM. polymorphaand has diverse physiological functions. We propose that MpLHT1 contributes to homeostasis of ACC and other amino acids inM. polymorphagrowth and reproduction.

     
    more » « less
  3. Summary

    The mechanisms that regulate the vast diversity of plant organ shapes such as the fruit remain to be fully elucidated. TONNEAU1 Recruiting Motif proteins (TRMs) have been implicated in the control of organ shapes in a number of plant species, including tomato. However, the role of many of them is unknown. TRMs interact with Ovate Family Proteins (OFPs) via the M8 domain. However, thein plantafunction of the TRM‐OFP interaction in regulating shape is unknown.

    We used CRISPR/Cas9 to generate knockout mutants in TRM proteins from different subclades and in‐frame mutants within the M8 domain to investigate their roles in organ shape and interactions with OFPs.

    Our findings indicate that TRMs impact organ shape along both the mediolateral and proximo‐distal axes of growth. Mutations inSltrm3/4andSltrm5act additively to rescue the elongated fruit phenotype ofovate/Slofp20(o/s) to a round shape. Contrary, mutations inSltrm19andSltrm17/20aresult in fruit elongation and further enhance the obovoid phenotype in theo/smutant.

    This study supports a combinatorial role of the TRM‐OFP regulon where OFPs and TRMs expressed throughout development have both redundant and opposing roles in regulating organ shape.

     
    more » « less
  4. Abstract

    Among CRISPR-Cas genome editing systems,Streptococcus pyogenesCas9 (SpCas9), sourced from a human pathogen, is the most widely used. Here, through in silico data mining, we have established an efficient plant genome engineering system using CRISPR-Cas9 from probioticLactobacillus rhamnosus. We have confirmed the predicted 5’-NGAAA-3’ PAM via a bacterial PAM depletion assay and showcased its exceptional editing efficiency in rice, wheat, tomato, and Larix cells, surpassing LbCas12a, SpCas9-NG, and SpRY when targeting the identical sequences. In stable rice lines, LrCas9 facilitates multiplexed gene knockout through coding sequence editing and achieves gene knockdown via targeted promoter deletion, demonstrating high specificity. We have also developed LrCas9-derived cytosine and adenine base editors, expanding base editing capabilities. Finally, by harnessing LrCas9’s A/T-rich PAM targeting preference, we have created efficient CRISPR interference and activation systems in plants. Together, our work establishes CRISPR-LrCas9 as an efficient and user-friendly genome engineering tool for diverse applications in crops and beyond.

     
    more » « less
  5. Summary

    Central metabolism produces amino and fatty acids for protein and lipids that establish seed value. Biosynthesis of storage reserves occurs in multiple organelles that exchange central intermediates including two essential metabolites, malate, and pyruvate that are linked by malic enzyme. Malic enzyme can be active in multiple subcellular compartments, partitioning carbon and reducing equivalents for anabolic and catabolic requirements. Prior studies based on isotopic labeling and steady‐state metabolic flux analyses indicated malic enzyme provides carbon for fatty acid biosynthesis in plants, though genetic evidence confirming this role is lacking. We hypothesized that increasing malic enzyme flux would alter carbon partitioning and result in increased lipid levels in soybeans.

    Homozygous transgenic soybean plants expressing Arabidopsis malic enzyme alleles, targeting the translational products to plastid or outside the plastid during seed development, were verified by transcript and enzyme activity analyses, organelle proteomics, and transient expression assays. Protein, oil, central metabolites, cofactors, and acyl‐acyl carrier protein (ACPs) levels were quantified overdevelopment.

    Amino and fatty acid levels were altered resulting in an increase in lipids by 0.5–2% of seed biomass (i.e. 2–9% change in oil).

    Subcellular targeting of a single gene product in central metabolism impacts carbon and reducing equivalent partitioning for seed storage reserves in soybeans.

     
    more » « less