Source: UNIVERSITY OF NEW HAMPSHIRE submitted to
ESTABLISHING GENE EDITING IN GENETICALLY INTRACTABLE MICROBES INVOLVED IN PLANT-MICROBE INTERACTIONS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
Reporting Frequency
Annual
Accession No.
1022255
Grant No.
2020-67014-31551
Cumulative Award Amt.
$283,550.00
Proposal No.
2019-07101
Multistate No.
(N/A)
Project Start Date
Sep 1, 2020
Project End Date
Aug 31, 2023
Grant Year
2020
Program Code
[A1191]- Agricultural Innovation through Gene Editing
Project Director
Tisa, L. S.
Recipient Organization
UNIVERSITY OF NEW HAMPSHIRE
51 COLLEGE RD SERVICE BLDG 107
DURHAM,NH 03824
Performing Department
MCBS
Non Technical Summary
Beneficial microbes are known to associate with plants as endophytes, symbionts or just closely located next to the plant in the rhizosphere. These relationships provide favorable effects on plant growth and health under stressed environment conditions and protection against pathogens. Many of these microbes are genetically intractable and difficult to study. Nitrogen fixation by actinorhizal and leguminous plants is an important part of the nitrogen budget of the planet. Actinorhizal plants provide an excellent mechanism to restore disrupted environmental sites. A major hindrance in the application of these association is the lack of genetic tools for the beneficial microbes associated with plants. The purpose of this study is the development of gene editing tools that will allow the genetic analysis of plant-associated microbes and their interactions with their host plants. The establishment of gene editing technology is a major step in manipulating these important beneficial plant-associated microbes and provide a greater understanding of the plant-microbe interactions including a variety of agricultural crops.
Animal Health Component
(N/A)
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20640101080100%
Knowledge Area
206 - Basic Plant Biology;

Subject Of Investigation
4010 - Bacteria;

Field Of Science
1080 - Genetics;
Goals / Objectives
A wide variety of microbes are associated with plants as endophytes, symbionts or just closed connected to the plant. Many of these microbes have beneficial effects on plant growth and health but have proved to be genetically intractable and difficult to study. The overall goal of this project is to establish gene editing approaches in bacteria that are genetically intractable. The bacterium, Frankia, is an example of one of these plant beneficial symbionts that is considered genetically intractable. It forms a nitrogen-fixing association with woody plants (termed actinorhizal plants) and ensures successful growth and survival of the plant in stressed environments. Nitrogen fixation by actinorhizal plants is an important part of the nitrogen budget of the planet. The plants are involved in land reclamation, reforestation, soil stabilization, landscaping, fuel, and as a food source for ruminant animals. The symbiotic association greatly accelerates growth of the host plant and indirectly does the same for neighboring plants. The goals of this project are: (1) Establishing the use of CRISPR-Cas9 for gene editing in Frankia and (2) Initiate protocol learned in Objective 1 to other genetically intractable actinobacteria. The project addresses the expansion of gene editing technologies for use in agriculturally-important microorganisms that are associated with plants and/or animals. The establishment of gene editing technology is a major step in manipulating these important beneficial plant-associated microbes that have been considered genetically intractable and understudied. These tools are necessary to provide a greater understanding of the plant-microbe interactions and may be extended to other microbes for a variety of crops. The discovery of gene editing approaches with these genetically difficult microbes could also have broader implications and beneficial effects in biotechnology technologies for use in agriculturally-important microorganisms that are associated with plants.
Project Methods
Building off our recent successfully efforts developing stable gene transfer protocols for a genetically intractable plant-associated actinobacteria, Frankia, we will focus on establishing gene editing or CRISPR-Cas9 in the genetically intractable Frankia as our first plant-associated microbe and this tool will be extended to other genetically intractable plant-associated actinobacteria.Objective 1. Establishing the use of CRISPR-Cas9 for gene editing in Frankia.Several modified CRISPR-Cas9 plasmids having different antibiotic resistance genes have been constructed. A synthesized Frankia 16S promoter was cloned in front of the Cas9 gene to allow expression of Cas9 gene in Frankia. The constructs have been successfully introduced and stability maintained in Frankia. The plasmid inside Frankia expresses Cas9 gene so we are at a good starting point to generate mutants by this gene editing approach. Potential genes involved in plant-microbe interactions or growth under harsh environmental conditions will serve as potential targets for the gene-editing experiments. To target a specific gene and generate a large deletion (starting with a 200-300 bp deletion), two editing templates are required for both ends of the targeted genes (1 Kbp each in length). Once generated, the mutants will be confirmed by molecular approaches and the physiological properties including plant infectivity will be determined.Objective 2. Initiate protocol learned in Objective 1 to other genetically intractable actinobacteriaWe will use lessons learned in Objective 1 to guide our efforts to utilize gene editing technology with other plant-associated actinobacteria. For these studies, we have initially chosen three different actinobacteria, Micromonospora strain L5, Nocardia casuarinae BMG51109, and Nocardia sp. strain BMG111209. Genome databases are available for all three actinobacteria. We have shown that the Nocardia strains are beneficial to plant health. Other plant-associated actinobacteria will also be included in these studies to expand the range of this gene editing tool. Several actinobacteria have been isolated from other plants and their genomes have been sequenced to provide background information for this gene editing tool.

Progress 09/01/20 to 08/31/23

Outputs
Target Audience:The actinorhizal symbiosis represents an important ecological and economic role in agriculture and the environment. The diversity of outcomes and impacts suggest that groups working on plant-microbe interactions (beneficial and pathogenic), agricultural and biotechnology industries, land restoration groups, environmental restoration and protection groups, farmers are projected target groups. The educational components of the project target the training of new investigators to agricultural and environmental sciences. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?For the duration of the project period, this grant has helped support the work of 3 graduate students (Megan Worth, Alex Gomez, and Ryan Wilmot), 1 postdoctoral fellow (Abdellatif Gueddou) and 2 undergraduate students (Hope Donahue, and Aiden Moser). Ms. Worth's PhD research is focused on the recognition of Frankia with its host actinorhizal plant and extending its host range. She has been generating CRISPR mutations in potential genes involved in this process and in copper tolerance by Frankia. Ms. Gomez's PhD research is focused on the bioremediation capacity of Frankia and she has been generating CRISPR mutants with defects in alkane degradation. Mr. Wilmot has been transferring CRISPR techniques to Blastococcus. Dr. Gueddou has been overseeing the entire project and has been generating CRISPR mutation in potential genes involved in plant host recognition. Hope Donahue, and Aiden Moser are undergraduate students, who have been involved in aiding the generation of the Frankia CRISPR mutants and testing their ability to re-infect host plants. How have the results been disseminated to communities of interest?Although the Covid pandemic has affected professional conferences, and some conferences are beginning to open up. The preliminary results of this study were presented at the 15th European Nitrogen Fixation Conference (ENFC 2023) held in Napoles, Italy August 31-September 3, 2023. The PI (Tisa) was on sabbatical in 2023 and presented the preliminary results of this research at various venues in four different countries Senegal, Fance, Tunisia and Argentina. Wehave one manuscript ready for submission and anticipate at least four more manuscripts from the results of this project. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Nitrogen fixation by plants is an important part of the nitrogen budget of the planet. Actinorhizal plants involved are also of economic significance with respect to land reclamation, reforestation, soil stabilization, landscaping, fuel, and as a food source for ruminant animals. Actinorhizal plants also provide an excellent mechanism to restore disrupted environmental sites. The ability of Frankia to bind and sequester several toxic heavy metals suggests potential for bioremediation and phytoremediation applications especially on heavy-metal-contaminated-land. A major hindrance in the application of this system is the lack of genetic tools for Frankia, the bacterial partner of the symbiosis. The purpose of this study is the development of gene editing tools that will allow the genetic and genomic analysis of genetically intractable microbes like Frankia. The overall impact of this study is a greater understanding of plant-microbe beneficial interactions. The use of these actinorhizal plants in bioremediation, soil stabilization, nurse cropping, biomass production, and land reclamation applications could potentially impact the 320 million people in the United States. Objective 1. Establishing the use of CRISPR-Cas9 for gene editing in Frankia. We constructed several modified CRISPR-Cas9 plasmids having different antibiotic resistance (chloramphenicol, gentamycin, or tetracycline) genes. The Streptomyces CRISPR-Cas system from pCRISPRomyces2 and the ori, rep and mob genes from pBBR1MCS plasmids were used in this construction. The pBBR1MCS plasmids are efficiently transferred and stably maintained in Frankia. A synthesized Frankia 16S promoter was cloned in front of the Cas9 gene to allow expression of Cas9 gene in Frankia. These constructs have been successfully introduced and stability maintained in Frankia. The plasmid inside Frankia expresses Cas9 gene. The CRISPR-Cas9 Frankia plasmid was further modified by altering the BbaI sites in the spacer cloning region to BsaI sites. This change allows Gateway cloning of the spacer into the modified CRISPR-Cas9 plasmid. Cloning at the BsaI site results in the loss of the lacZ gene and positive selection through blue/white recognition of colonies on X-gal growth medium. Two modified CRISPR-Cas9 plasmids were designed FR1 (chloramphenicol resistance) and FR3(tetracycline resistance). Plasmids FR1 and FR3 were introduced into Frankia casuarinae strain CcI3 at a frequency of 3.1 x 10-3 and 1.9 x 10-3 transformants per total CFU, respectively and stably maintained. End-point RT-PCR results showed that the Cas9 gene was expressed in Frankia. As a proof of concept, genes for the hopanoid biosynthesis cluster in F. casuarinae strain CcI3 were targeted. The hpnC (francci3_0819) gene encodes the squalene/phytoene synthase, which is the first gene in the hopanoid operon involved in its biosynthesis. The PAM site was identified, and a spacer was generated. Editing templates were generated by PCR that should result in the deletion of 241 bp within the hpnC gene. Frankia hpnC mutants were generated by FR1 construct at a frequency of 5.9 x 10-4 transformants per CFU. The hpnC mutants were confirmed by several molecular approaches. First, the target hpnC gene was sequenced and showed the expected 241 bp deletion. Second, PCR of the hpnC gene produced an amplicon that was smaller in the mutant compared to the wild type. Third, end-point RT-PCR demonstrated that the hpnC gene was not expressed in the mutant. The genome of the hpnC mutants were re-sequenced to look for second site mutations which were absent, but also confirmed the 241 bp deletion in the hpnC gene. The physiological properties of the hpnC mutant were investigated. The hpn operon is involved in the biosynthesis of hopanoids, which are lipids that protect nitrogenase from oxygen inactivation. Hopanoids surround vesicles, nitrogen-fixing structure, of the microbe and visually appear as a phase bright material surrounding the vesicle. HpnC mutants had altered vesicle production, resulting in lower numbers of phase dark vesicle and absence of nitrogenase activity under atmosphere oxygen conditions. The hopanoid content of the hpnC mutants and their parental wild type were measured. The hpnC mutants produced drastically reduced levels of diploptene and diplopterol compared to the parental wild type but produced similar levels of squalene the precursor to the biosynthetic pathway. This result indicates that the mutants were defective hopanoid biosynthesis. The effect of plant infectivity was also tested on its actinorhizal host plant. Compared to the wild type and wild type containing the pFR1, hpnC mutants produced reduced drastically nodulation or no nodules on the plants and resulted in poor plant health similar to uninoculated control plants. These results show that hopanoids may play a role in the infection process for actinorhizal plants. We have also generated another F. casuarinae strain CcI3 mutant by deleting 214 bp of the que (francci3_1753) gene. This gene encodes a product in the queuosine biosyhtetic pathway. This natural product has been implicated Sinorhizobium meliloti symbioisis. The mutant was confirmed by molecular approaches and preliminary plant infectivity experiments indicate that it is defective in plant nodulation. Mutations in two genes, hboN and lmbE (GlcNAc-PI de-N-acetylase), potentially involved in the plant infection process have been constructed and are being confirmed by molecular approaches. Currently, we are targeting several other genes for gene editing in other Frankia species. In Frankia inefficax EuI1c, three genes (copA, copD, and FraEuIc_1092) predicted to be involved in copper tolerance and have been targeted. Mutations of the these three genes have been generated and are being confirmed by molecular approaches and further physiological studies. In both Frankia sp. CN3 and Frankia alni ACN14a, the alkane-1-monooxygenase genes (FrCN3DRAFT_5621 and FRAAL1986, respectively) are predicted to be involved in alkane degradation. The constrict of these mutations by gene edited are currently in progress. Objective 2. Initiate protocol learned in Objective 1 to other genetically intractable actinobacteria We have initiated studies on developing CRISPR use in other actinobacteria including Blastococcus, Rhodococcus, and Nocardia. These bacteria appear to be more amendable to electroporation technology, so we are introducing the construction via that mechanism. We have introduced pFR1 into Blastococcus saxobsidens DD2 by electroporation and a targeting specific genes for gene editing to show that the protocol is working outside of Frankia.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: L. S. Tisa. 2023 Bacteria and environmental biology: from Frankia genetics and genomics in actinorhizal symbiosis to the impact of climate on the global microbiome of stones Departamento de Ciencia y Tecnolog�a, Universidad Nacional de Quilmes and researchers from Buenos Aires and La Plata Bernal, Argentina August 11,2023
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: L. S. Tisa. 2023.Bacteria and environmental biology: from Frankia genetics and genomics in actinorhizal symbiosis to the impact of climate on the global microbiome of stones University of University of Cheikh Anta Diop, Dakar Senegal February 21, 2023.
  • Type: Conference Papers and Presentations Status: Submitted Year Published: 2023 Citation: L. S. Tisa. 2023 Genetic and Genomics approach to the actinorhizal symbiosis IRD, CIRCAD and ISRA Dakar, Senegal February 23, 2023.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: L. S. Tisa. 2023 Bacteria and environmental biology: from Frankia genetics and genomics in actinorhizal symbiosis to the impact of climate on the global microbiome of stones IRD Montpellier, France March 23, 2023
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2023 Citation: Abdellatif Gueddou, Megan Gracia, and Louis S. Tisa. 2023. Investigating Early Actinorhizal Signaling: Probing the Functional Consequences of GlcNAc-PI De-N-Acetylase Gene Knockout in Frankia casuarinae CcI3T via CRISPR/Cas9. The 4th Tunisian Association of Microbiology Ecology ( ATEM) International Conference on Microbial Ecology: From Microbial Lifestyles to Styling Ecosystems in Hammamet, Tunisa December, 7-10, 2023
  • Type: Journal Articles Status: Other Year Published: 2023 Citation: Pesce, C., V. KLEINER, M. WORTH, H. Pan, L. FREIDMAN, B. Berlin, and L.S. Tisa. Targeted mutagenesis in Frankia casuarinae strain CcI3 through the gene editing CRISPR/Cas9 system. To be submitted Appl. Environ. Microbiol.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Megan Gracia, Abdellatif Gueddou and Louis S. Tisa. 2023. Investigating copper tolerance in Frankia ineficax EuI1c through targeted mutagenesis. 15th European Nitrogen Fixation Conference (ENFC 2023) held in Napoles, Italy August 31-September 3, 2023


Progress 09/01/21 to 08/31/22

Outputs
Target Audience:The actinorhizal symbiosis represents an important ecological and economic role in agriculture and the environment. The diversity of outcomes and impacts suggest that groups working on plant-microbe interactions (beneficial and pathogenic), agricultural and biotechnology industries, land restoration groups, environmental restoration and protection groups, farmers are projected target groups. The educational components of the project target the training of new investigators to agricultural and environmental sciences. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?For the duration of the project period, this grant has helped support the work of 3 graduate students (Megan Worth, Alex Gomez, and Ryan Wilmot), 1 postdoctoral fellow (Abdellatif Gueddou) and 2 undergraduate students (Hope Donahue, and Aiden Moser). Ms. Worth's PhD research is focused on the recognition of Frankia with its host actinorhizal plant and extending its host range. She has been generating CRISPR mutations in potential genes involved in this process and in copper tolerance by Frankia. Ms. Gomez's PhD research is focused on the bioremediation capacity of Frankia and she has been generating CRISPR mutants with defects in alkane degradation. Mr. Wilmot has been transferring CRISPR techniques to Blastococcus. Dr. Gueddou has been overseeing the entire project and has been generating CRISPR mutation in potential genes involved in plant host recognition. Hope Donahue, and Aiden Moser are undergraduate students, who have been involved in aiding the generation of the Frankia CRISPR mutants and testing their ability to re-infect host plants. How have the results been disseminated to communities of interest?Although the Covid pandemic has affected professional conferences and some conferences are beginning to open up. The preliminary results of this study were presented at the 28th North American Symbiotic Nitrogen Fixation Conference on June 5-8, 2022 in Madison, WI. I anticipate that more professional meetings will be available this upcoming year. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Nitrogen fixation by plants is an important part of the nitrogen budget of the planet. Actinorhizal plants involved are also of economic significance with respect to land reclamation, reforestation, soil stabilization, landscaping, fuel, and as a food source for ruminant animals. Actinorhizal plants also provide an excellent mechanism to restore disrupted environmental sites. The ability of Frankia to bind and sequester several toxic heavy metals suggests potential for bioremediation and phytoremediation applications especially on heavy-metal-contaminated-land. A major hindrance in the application of this system is the lack of genetic tools for Frankia, the bacterial partner of the symbiosis. The purpose of this study is the development of gene editing tools that will allow the genetic and genomic analysis of genetically intractable microbes like Frankia. The overall impact of this study is a greater understanding of plant-microbe beneficial interactions. The use of these actinorhizal plants in bioremediation, soil stabilization, nurse cropping, biomass production, and land reclamation applications could potentially impact the 320 million people in the United States. Objective 1. Establishing the use of CRISPR-Cas9 for gene editing in Frankia. Building off our success in developing gene transfer in Frankia, we constructed several modified CRISPR-Cas9 plasmids having different antibiotic resistance (chloramphenicol, gentamycin, or tetracycline) genes. The Streptomyces CRISPR-Cas system from pCRISPRomyces2 and the ori, rep and mob genes from pBBR1MCS plasmids were used in this construction. The pBBR1MCS plasmids are efficiently transferred and stably maintained in Frankia. A synthesized Frankia 16S promoter was cloned in front of the Cas9 gene to allow expression of Cas9 gene in Frankia. These constructs have been successfully introduced and stability maintained in Frankia. The plasmid inside Frankia expresses Cas9 gene. The CRISPR-Cas9 Frankia plasmid was further modified by altering the BbaI sites in the spacer cloning region to BsaI sites. This change allows Gateway cloning of the spacer into the modified CRISPR-Cas9 plasmid. Cloning at the BsaI site results in the loss of the lacZ gene and positive selection through blue/white recognition of colonies on X-gal growth medium. Two modified CRISPR-Cas9 plasmids were designed FR1 (chloramphenicol resistance) and FR3(tetracycline resistance). Plasmids FR1 and FR3 were introduced into Frankia casuarinae strain CcI3 at a frequency of 3.1 x 10-3 and 1.9 x 10-3 transformants per total CFU, respectively and stably maintained. End-point RT-PCR results showed that the Cas9 gene was expressed in Frankia. As a proof of concept, genes for the hopanoid biosynthesis cluster in F. casuarinae strain CcI3 were targeted. The hpnC (francci3_0819) gene encodes the squalene/phytoene synthase, which is the first gene in the hopanoid operon involved in its biosynthesis. The PAM site was identified, and a spacer was generated. Editing templates were generated by PCR that should result in the deletion of 241 bp within the hpnC gene. Frankia hpnC mutants were generated by FR1 construct at a frequency of 5.9 x 10-4 transformants per CFU. The hpnC mutants were confirmed by several molecular approaches. First, the target hpnC gene was sequenced and showed the expected 241 bp deletion. Second, PCR of the hpnC gene produced an amplicon that was smaller in the mutant compared to the wild type. Third, end-point RT-PCR demonstrated that the hpnC gene was not expressed in the mutant. The genome of the hpnC mutants were re-sequenced to look for second site mutations which were absent, but also confirmed the 241 bp deletion in the hpnC gene. The physiological properties of the hpnC mutant were investigated. The hpn operon is involved in the biosynthesis of hopanoids, which are lipids that protect nitrogenase from oxygen inactivation. Hopanoids surround vesicles, nitrogen-fixing structure, of the microbe and visually appear as a phase bright material surrounding the vesicle. HpnC mutants had altered vesicle production, resulting in lower numbers of phase dark vesicle and absence of nitrogenase activity under atmosphere oxygen conditions. The hopanoid content of the hpnC mutants and their parental wild type were measured. The hpnC mutants produced drastically reduced levels of diploptene and diplopterol compared to the parental wild type but produced similar levels of squalene the precursor to the biosynthetic pathway. This result indicates that the mutants were defective hopanoid biosynthesis. The effect of plant infectivity was also tested on its actinorhizal host plant. Compared to the wild type and wild type containing the pFR1, hpnC mutants produced reduced drastically nodulation or no nodules on the plants and resulted in poor plant health similar to uninoculated control plants. These results show that hopanoids may play a role in the infection process for actinorhizal plants. We have also generated another F. casuarinae strain CcI3 mutant by deleting 214 bp of the que (francci3_1753) gene. This gene encodes a product in the queuosine biosyhtetic pathway. This natural product has been implicated Sinorhizobium meliloti symbioisis. The mutant was confirmed by molecular approaches and preliminary plant infectivity experiments indicate that it is defective in plant nodulation. Two genes (hboN and another gene) potentially involved in the plant infection process have been targeted and are in progress. Currently, we are targeting several other genes for gene editing in other Frankia species. Four genes in Frankia inefficax EuI1c predicted to be involved in copper tolerance have been targeted and are currently being gene edited. Genes predicted to be involved in alkane degradation Frankia sp. EUN1f and Frankia alni ACN14a ae inprogress. Objective 2. Initiate protocol learned in Objective 1 to other genetically intractable actinobacteria We have initiated studies on developing CRISPR use in other actinobacteria including Blastococcus, Rhodococcus, and Nocardia. These bacteria appear to be more amendable to electroporation technology, so we are introducing the construction via that mechanism. We have introduced pFR1 into Blastococcus saxobsidens DD2 by electroporation and a targeting specific genes for gene editing to show that the protocol is working outside of Frankia.

Publications

  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2022 Citation: Tisa, L.S. C. Pesce, V. Kleiner and M. Worth. 2022. Genetic tools in Frankia: Yes we can, from complementation to site-specific mutagenesis. The 28th North American Symbiotic Nitrogen Fixation Conference. June 5-8, 2022 Madison, WI (Invited Talk)


Progress 09/01/20 to 08/31/21

Outputs
Target Audience:The actinorhizal symbiosis represents an important ecological and economic role in agriculture and the environment. The diversity of outcomes and impacts suggest that groups working on plant-microbe interactions (beneficial and pathogenic), agricultural and biotechnology industries, land restoration groups, environmental restoration and protection groups, farmers are projected target groups. The educational components of the project target the training of new investigators to agricultural and environmental sciences. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?For the duration of the project period, this grant has helped support the work of 1 graduate student (Megan Worth), and 2 undergraduate students (Lilly Friedman, and Kelsey Mercurio). Ms. Worth's PhD research is focused on the recognition of Frankia with its host actinorhizal plant and extending its host range. She has been generating CRISPR mutations in potential genes involved in this process. Lilly Friedman and Kelsey Mercurio are undergraduate students, who have been involved in aiding the generation of the Frankia CRISPR mutants and testing their ability to re-infect host plants. How have the results been disseminated to communities of interest?The Covid pandemic affected professional conferences and several canceled or postponed. The 20th International Conference on Frankia and Actinorhizal Plants was held virtually, and the preliminary results of this study were presented there. Preliminary results were also presented locally (Friedman, L., C. Pesce, M. Worth and L. S. Tisa. 2021. Gene editing in Actinobacteria. The 30th Annual COLSA Undergraduate Research Conference, April 24th. 2021). I anticipate that more professional meetings are being available this upcoming year. What do you plan to do during the next reporting period to accomplish the goals?The arrival of my postdoctoral fellow will help to accomplis all of the goals in objective one and intiate objective two. No changes in these plans are anticipated.

Impacts
What was accomplished under these goals? As preface to this section, I would like to point out that the pandemic caused serious delays in the progress of this project. The postdoctoral fellow hired for this project had a major delay in obtaining a visa because the embassy was shut down. They did not arrive until September 2021. Since their arrival, work has progressed significantly. Nitrogen fixation by plants is an important part of the nitrogen budget of the planet. Actinorhizal plants involved are also of economic significance with respect to land reclamation, reforestation, soil stabilization, landscaping, fuel, and as a food source for ruminant animals. Actinorhizal plants also provide an excellent mechanism to restore disrupted environmental sites. The ability of Frankia to bind and sequester several toxic heavy metals suggests potential for bioremediation and phytoremediation applications especially on heavy-metal-contaminated-land. A major hindrance in the application of this system is the lack of genetic tools for Frankia, the bacterial partner of the symbiosis. The purpose of this study is the development of gene editing tools that will allow the genetic and genomic analysis of genetically intractable microbes like Frankia. The overall impact of this study is a greater understanding of plant-microbe beneficial interactions. The use of these actinorhizal plants in bioremediation, soil stabilization, nurse cropping, biomass production, and land reclamation applications could potentially impact the 320 million people in the United States. Objective 1. Establishing the use of CRISPR-Cas9 for gene editing in Frankia. Building off our success in developing gene transfer in Frankia, we constructed several modified CRISPR-Cas9 plasmids having different antibiotic resistance (chloramphenicol, gentamycin, or tetracycline) genes. The Streptomyces CRISPR-Cas system from pCRISPRomyces2 and the ori, rep and mob genes from pBBR1MCS plasmids were used in this construction. The pBBR1MCS plasmids are efficiently transferred and stably maintained in Frankia. A synthesized Frankia 16S promoter was cloned in front of the Cas9 gene to allow expression of Cas9 gene in Frankia. The constructs have been successfully introduced and stability maintained in Frankia. The plasmid inside Frankia expresses Cas9 gene. The CRISPR-Cas9 Frankia plasmid was further modified by altering the BbaI sites in the spacer cloning region to BsaI sites. This change allows Gateway cloning of the spacer into the modified CRISPR-Cas9 plasmid. Cloning at the BsaI site results in the loss of the lacZ gene and positive selection through blue/white recognition of colonies on X-gal growth medium. Two modified CRISPR-Cas9 plasmids were designed FR1 (chloramphenicol resistance) and FR3(tetracycline resistance). Plasmids FR1 and FR3 were introduced into Frankia casuarinae strain CcI3 at a frequency of 3.1 x 10-3 and 1.9 x 10-3 transformants per total CFU, respectively and stably maintained. End-point RT-PCR results showed that the Cas9 gene was expressed in Frankia. As a proof of concept, genes for the hopanoid biosynthesis cluster in F. casuarinae strain CcI3 were targeted. The hpnC (francci3_0819) gene encodes the squalene/phytoene synthase, which is the first gene in the hopanoid operon involved in its biosynthesis. The PAM site was identified, and a spacer was generated. Editing templates were generated by PCR that should result in the deletion of 241 bp within the hpnC gene. Frankia hpnC mutants were generated by FR1 construct at a frequency of 5.9 x 10-4 transformants per CFU. The hpnC mutants were confirmed by several molecular approaches. First, the target hpnC gene was sequenced and showed the expected 241 bp deletion. Second, PCR of the hpnC gene produced an amplicon that was smaller in the mutant compared to the wild type. Third, end-point RT-PCR demonstrated that the hpnC gene was not expressed in the mutant. The genome of the hpnC mutants were re-sequenced to look for second site mutations which were absence, but also conformed the 241 bp deletion in the hpnC gene. The physiological properties of the hpnC mutant were investigated. The hpn operon involved in the biosynthesis of hopanoids, which are lipids that protect nitrogenase from oxygen inactive. Hopanoids surround vesicles, nitrogen-fixing structure, of the microbe and visually appear as a phase bright material surrounding the vesicle. HpnC mutants had altered vesicle production, resulting in lower numbers of phase dark vesicle and absence of nitrogenase activity under atmosphere oxygen conditions. The effect of plant infectivity was also tested on its actinorhizal host plant. Compared to the wild type and wild type containing the FR1, hpnC mutants produced reduced drastically nodulation or no nodules on the plants and resulted in poor plant health similar to uninoculated control plants. These results show that hopanoids may play a role in the infection process for actinorhizal plants. We have also generated another F. casuarinae strain CcI3 mutant by deleting 214 bp of the que (francci3_1753) gene. This gene encodes a product in the queuosine biosyhtetic pathway. This natural product has been implicated Sinorhizobium meliloti symbioisis. The mutant was confirmed by molecular approaches and preliminary plant infectivity experiments indicate that it defective in plant nodulation. Currently, we targeting several other genes for gene editing in other Frankia species. Objective 2. Initiate protocol learned in Objective 1 to other genetically intractable actinobacteria We have not initiated this objective yet, but will once we confirm the ability to use it in other Frankia species.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 20221 Citation: Celine Pesce, Victoria Kleiner, Lilly Friedman, Megan Worth, and Louis S. Tisa. 2021. Genetic tools in Frankia: Yes we can, from complementation to site-specific mutagenesis Frankia. The 20th Symposium on Frankia and Actinorhizal Plants. May 29, 2021 Japan (Invited Talk: Zoom meeting)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Friedman, L., C. Pesce, M. Worth and L. S. Tisa. 2021. Gene editing in Actinobacteria. The 30th Annual COLSA Undergraduate Research Conference, April 24th. 2021.