Plant hemoglobins (Hbs) have been identified and characterized in the nitrogen-fixing root nodule... more Plant hemoglobins (Hbs) have been identified and characterized in the nitrogen-fixing root nodules of legumes and some nonlegumes, including Parasponia nodulated by Rhizobium and actinorhizal plants that undergo symbiosis with the actinomycete Frankia. The role of Hb in symbiosis is to supply oxygen to the bacterial respiration chain while preserving the activity of the oxygen-intolerant nitrogenase enyme complex. Besides the symbiotic hb genes which are expressed specifically in nitrogen-fixing nodules, a second type of hb genes has been isolated in nodulating and nonnodulating plants: in soybean, the actinorhizal tree Casuarina glauca, Trema tomentosa, a nonnodulating relative of Parasponia and in cereals such as barley, wheat, maize and rice. These genes are expressed in different tissues such as roots, stems and seeds.
Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), threatens glob... more Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), threatens global food security and the livelihood of small-scale rice producers. Analyses of Xoo collections from Asia, Africa and the Americas demonstrated complete continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemic African Xoo, carry Asian-type TAL effectors targeting the sucrose transporter SWEET11a and iTALes suppressing Xa1. Phylogenomics clustered these strains with Xoo from Southern-China. African rice varieties do not carry effective resistance. To protect African rice production against this emerging threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit all known TALe-binding elements in three SWEET promoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains of Xoo, including strains recently discovered in Tanz...
This dataset contains additional supporting information and source code related to the discovery ... more This dataset contains additional supporting information and source code related to the discovery of Xanthomonas-induced small RNAs (xisRNAs) as described in the Related Publication. Deep small RNA (sRNA) sequencing analysis discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae pathovars. A set of 163 xisRNAs loci were distinctively upregulated in response to various bacterial strains at an early stage of infection. Most xisRNA loci overlap with annotated cis-transcripts sequences often encoding protein kinase domain proteins including RLKs and RLCKs. A number of the corresponding rice cis-genes have documented functions in immune signaling and about one third of the xisRNA loci coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. Notably xisRNAs production was dependent on the X. or...
Biological Nitrogen Fixation for the 21st Century, 1998
Plant hemoglobins (Hbs) have been identified and characterized in the nitrogen-fixing root nodule... more Plant hemoglobins (Hbs) have been identified and characterized in the nitrogen-fixing root nodules of legumes and some nonlegumes, including Parasponia nodulated by Rhizobium and actinorhizal plants that undergo symbiosis with the actinomycete Frankia. The role of Hb in symbiosis is to supply oxygen to the bacterial respiration chain while preserving the activity of the oxygen-intolerant nitrogenase enyme complex. Besides the symbiotic hb genes which are expressed specifically in nitrogen-fixing nodules, a second type of hb genes has been isolated in nodulating and nonnodulating plants: in soybean, the actinorhizal tree Casuarina glauca, Trema tomentosa, a nonnodulating relative of Parasponia and in cereals such as barley, wheat, maize and rice. These genes are expressed in different tissues such as roots, stems and seeds.
The bacterial plant pathogen Xanthomonas oryzae pv. oryzae is responsible for the foliar rice bac... more The bacterial plant pathogen Xanthomonas oryzae pv. oryzae is responsible for the foliar rice bacterial blight disease. Genetically contrasted, continent-specific, sublineages of this species can cause important damages to rice production both in Asia and Africa. We report on the genome of the CIX2779 strain of this pathogen, previously named NAI1 and originating from Niger. Oxford Nanopore long reads assembly and Illumina short reads polishing produced a genome sequence composed of a 4,725,792-bp circular chromosome and a 39,798-bp-long circular plasmid designated pCIX2779_1. The chromosome structure and base-level sequence are highly related to reference strains of African X. oryzae pv. oryzae and encode identical transcription activator-like effectors for virulence. Importantly, our in silico analysis strongly indicates that pCIX2779_1 is a genuine conjugative plasmid, the first indigenous one sequenced from an African strain of the X. oryzae species. [Formula: see text] Copyrigh...
Bacterial blight of rice is an important disease in Asia and Africa. The pathogen,Xanthomonas ory... more Bacterial blight of rice is an important disease in Asia and Africa. The pathogen,Xanthomonas oryzaepv.oryzae(Xoo), secretes one or more of six known transcription-activator-like effectors (TALes) that bind specific promoter sequences and induce, at minimum, one of the three host sucrose transporter genesSWEET11,SWEET13andSWEET14, the expression of which is required for disease susceptibility. We used CRISPR–Cas9-mediated genome editing to introduce mutations in all threeSWEETgene promoters. Editing was further informed by sequence analyses of TALe genes in 63Xoostrains, which revealed multiple TALe variants forSWEET13alleles. Mutations were also created inSWEET14, which is also targeted by two TALes from an AfricanXoolineage. A total of five promoter mutations were simultaneously introduced into the rice line Kitaake and the elite mega varieties IR64 and Ciherang-Sub1. Paddy trials showed that genome-editedSWEETpromoters endow rice lines with robust, broad-spectrum resistance.
Rice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa. Manag... more Rice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa. Management of RYMV is challenging. Genetic resistance provides the most effective and environment-friendly control. The recessive resistance locus rymv2 (OsCPR5.1) had been identified in African rice (O. glaberrima), however, introgression into O. sativa ssp. japonica and indica remains challenging due to crossing barriers. Here, we evaluated whether CRISPR/Cas9 genome editing of the two rice nucleoporin paralogs OsCPR5.1 (RYMV2) and OsCPR5.2 can be used to introduce RYMV resistance into the japonica variety Kitaake. Both paralogs had been shown to complement the defects of the Arabidopsis atcpr5 mutant, indicating partial redundancy. Despite striking sequence and structural similarities between the two paralogs, only oscpr5.1 loss-of-function mutants were fully resistant, while loss-of-function oscpr5.2 mutants remained susceptible, intimating that OsCPR5.1 plays a specific role in RYMV susc...
Xanthomonas oryzae pv. oryzae (Xoo) strains that cause bacterial leaf blight (BLB) limit rice (Or... more Xanthomonas oryzae pv. oryzae (Xoo) strains that cause bacterial leaf blight (BLB) limit rice (Oryza sativa) production and require breeding more resistant varieties. Transcription activator-like effectors (TALEs) activate transcription to promote leaf colonization by binding to specific plant host DNA sequences termed effector binding elements (EBEs). Xoo major TALEs universally target susceptibility genes of the SWEET transporter family. TALE-unresponsive alleles of clade III OsSWEET susceptibility gene promoter created with genome editing confer broad resistance on Asian Xoo strains. African Xoo strains rely primarily on the major TALE TalC, which targets OsSWEET14. Although the virulence of a talC mutant strain is severely impaired, abrogating OsSWEET14 induction with genome editing does not confer equivalent resistance on African Xoo. To address this contradiction, we postulated the existence of a TalC target susceptibility gene redundant with OsSWEET14. Bioinformatics analysis...
The islet of Gozo, Malta is known for its rural landscapes and attractive tourist destinations. I... more The islet of Gozo, Malta is known for its rural landscapes and attractive tourist destinations. It is also home to a variation of honeybees, maintained by the beekeepers of Gozo, and desired by farmers for the purpose of pollination. In July of 2016, I spent three weeks on this islet, practicing skills in applied anthropology through the Off the Beaten Track field school. I was interested in the means of production that go into the creation of honeybee products, and specifically the people that make this process possible. During my time in Gozo I met Adam, a 60-year-old beekeeper, who provided me with some of his perspectives on honeybee production. Working alongside Adam and his honeybees offered me a glimpse at what it means to be a keeper in Gozo. Recently this practice is experiencing new challenges, shaping the tasks and concerns of Gozitan beekeepers. These keepers express their perceptions of potential bee extinction as signs of colony collapse disorder (CCD) arise. With this, Gozo’s environment is facing unfamiliar conditions that are potentially related to climate change. These issues are ultimately met by a community of beekeepers that survives the practice of beekeeping on Gozo through the exchange of local knowledge and dialogue. I left Gozo with further questions about how the islet’s environment shapes beekeeping and what the future of this practice will look like given our warming planet.
Non-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, develo... more Non-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant–microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20–22 nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences, with about half of them encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and xisRNA loci predominantly coincide w...
ABSTRACTNon-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth... more ABSTRACTNon-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant-microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20-22nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences often encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and some xisRNA loci coincide with the coding sequen...
Plant hemoglobins (Hbs) have been identified and characterized in the nitrogen-fixing root nodule... more Plant hemoglobins (Hbs) have been identified and characterized in the nitrogen-fixing root nodules of legumes and some nonlegumes, including Parasponia nodulated by Rhizobium and actinorhizal plants that undergo symbiosis with the actinomycete Frankia. The role of Hb in symbiosis is to supply oxygen to the bacterial respiration chain while preserving the activity of the oxygen-intolerant nitrogenase enyme complex. Besides the symbiotic hb genes which are expressed specifically in nitrogen-fixing nodules, a second type of hb genes has been isolated in nodulating and nonnodulating plants: in soybean, the actinorhizal tree Casuarina glauca, Trema tomentosa, a nonnodulating relative of Parasponia and in cereals such as barley, wheat, maize and rice. These genes are expressed in different tissues such as roots, stems and seeds.
Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), threatens glob... more Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), threatens global food security and the livelihood of small-scale rice producers. Analyses of Xoo collections from Asia, Africa and the Americas demonstrated complete continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemic African Xoo, carry Asian-type TAL effectors targeting the sucrose transporter SWEET11a and iTALes suppressing Xa1. Phylogenomics clustered these strains with Xoo from Southern-China. African rice varieties do not carry effective resistance. To protect African rice production against this emerging threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit all known TALe-binding elements in three SWEET promoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains of Xoo, including strains recently discovered in Tanz...
This dataset contains additional supporting information and source code related to the discovery ... more This dataset contains additional supporting information and source code related to the discovery of Xanthomonas-induced small RNAs (xisRNAs) as described in the Related Publication. Deep small RNA (sRNA) sequencing analysis discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae pathovars. A set of 163 xisRNAs loci were distinctively upregulated in response to various bacterial strains at an early stage of infection. Most xisRNA loci overlap with annotated cis-transcripts sequences often encoding protein kinase domain proteins including RLKs and RLCKs. A number of the corresponding rice cis-genes have documented functions in immune signaling and about one third of the xisRNA loci coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. Notably xisRNAs production was dependent on the X. or...
Biological Nitrogen Fixation for the 21st Century, 1998
Plant hemoglobins (Hbs) have been identified and characterized in the nitrogen-fixing root nodule... more Plant hemoglobins (Hbs) have been identified and characterized in the nitrogen-fixing root nodules of legumes and some nonlegumes, including Parasponia nodulated by Rhizobium and actinorhizal plants that undergo symbiosis with the actinomycete Frankia. The role of Hb in symbiosis is to supply oxygen to the bacterial respiration chain while preserving the activity of the oxygen-intolerant nitrogenase enyme complex. Besides the symbiotic hb genes which are expressed specifically in nitrogen-fixing nodules, a second type of hb genes has been isolated in nodulating and nonnodulating plants: in soybean, the actinorhizal tree Casuarina glauca, Trema tomentosa, a nonnodulating relative of Parasponia and in cereals such as barley, wheat, maize and rice. These genes are expressed in different tissues such as roots, stems and seeds.
The bacterial plant pathogen Xanthomonas oryzae pv. oryzae is responsible for the foliar rice bac... more The bacterial plant pathogen Xanthomonas oryzae pv. oryzae is responsible for the foliar rice bacterial blight disease. Genetically contrasted, continent-specific, sublineages of this species can cause important damages to rice production both in Asia and Africa. We report on the genome of the CIX2779 strain of this pathogen, previously named NAI1 and originating from Niger. Oxford Nanopore long reads assembly and Illumina short reads polishing produced a genome sequence composed of a 4,725,792-bp circular chromosome and a 39,798-bp-long circular plasmid designated pCIX2779_1. The chromosome structure and base-level sequence are highly related to reference strains of African X. oryzae pv. oryzae and encode identical transcription activator-like effectors for virulence. Importantly, our in silico analysis strongly indicates that pCIX2779_1 is a genuine conjugative plasmid, the first indigenous one sequenced from an African strain of the X. oryzae species. [Formula: see text] Copyrigh...
Bacterial blight of rice is an important disease in Asia and Africa. The pathogen,Xanthomonas ory... more Bacterial blight of rice is an important disease in Asia and Africa. The pathogen,Xanthomonas oryzaepv.oryzae(Xoo), secretes one or more of six known transcription-activator-like effectors (TALes) that bind specific promoter sequences and induce, at minimum, one of the three host sucrose transporter genesSWEET11,SWEET13andSWEET14, the expression of which is required for disease susceptibility. We used CRISPR–Cas9-mediated genome editing to introduce mutations in all threeSWEETgene promoters. Editing was further informed by sequence analyses of TALe genes in 63Xoostrains, which revealed multiple TALe variants forSWEET13alleles. Mutations were also created inSWEET14, which is also targeted by two TALes from an AfricanXoolineage. A total of five promoter mutations were simultaneously introduced into the rice line Kitaake and the elite mega varieties IR64 and Ciherang-Sub1. Paddy trials showed that genome-editedSWEETpromoters endow rice lines with robust, broad-spectrum resistance.
Rice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa. Manag... more Rice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa. Management of RYMV is challenging. Genetic resistance provides the most effective and environment-friendly control. The recessive resistance locus rymv2 (OsCPR5.1) had been identified in African rice (O. glaberrima), however, introgression into O. sativa ssp. japonica and indica remains challenging due to crossing barriers. Here, we evaluated whether CRISPR/Cas9 genome editing of the two rice nucleoporin paralogs OsCPR5.1 (RYMV2) and OsCPR5.2 can be used to introduce RYMV resistance into the japonica variety Kitaake. Both paralogs had been shown to complement the defects of the Arabidopsis atcpr5 mutant, indicating partial redundancy. Despite striking sequence and structural similarities between the two paralogs, only oscpr5.1 loss-of-function mutants were fully resistant, while loss-of-function oscpr5.2 mutants remained susceptible, intimating that OsCPR5.1 plays a specific role in RYMV susc...
Xanthomonas oryzae pv. oryzae (Xoo) strains that cause bacterial leaf blight (BLB) limit rice (Or... more Xanthomonas oryzae pv. oryzae (Xoo) strains that cause bacterial leaf blight (BLB) limit rice (Oryza sativa) production and require breeding more resistant varieties. Transcription activator-like effectors (TALEs) activate transcription to promote leaf colonization by binding to specific plant host DNA sequences termed effector binding elements (EBEs). Xoo major TALEs universally target susceptibility genes of the SWEET transporter family. TALE-unresponsive alleles of clade III OsSWEET susceptibility gene promoter created with genome editing confer broad resistance on Asian Xoo strains. African Xoo strains rely primarily on the major TALE TalC, which targets OsSWEET14. Although the virulence of a talC mutant strain is severely impaired, abrogating OsSWEET14 induction with genome editing does not confer equivalent resistance on African Xoo. To address this contradiction, we postulated the existence of a TalC target susceptibility gene redundant with OsSWEET14. Bioinformatics analysis...
The islet of Gozo, Malta is known for its rural landscapes and attractive tourist destinations. I... more The islet of Gozo, Malta is known for its rural landscapes and attractive tourist destinations. It is also home to a variation of honeybees, maintained by the beekeepers of Gozo, and desired by farmers for the purpose of pollination. In July of 2016, I spent three weeks on this islet, practicing skills in applied anthropology through the Off the Beaten Track field school. I was interested in the means of production that go into the creation of honeybee products, and specifically the people that make this process possible. During my time in Gozo I met Adam, a 60-year-old beekeeper, who provided me with some of his perspectives on honeybee production. Working alongside Adam and his honeybees offered me a glimpse at what it means to be a keeper in Gozo. Recently this practice is experiencing new challenges, shaping the tasks and concerns of Gozitan beekeepers. These keepers express their perceptions of potential bee extinction as signs of colony collapse disorder (CCD) arise. With this, Gozo’s environment is facing unfamiliar conditions that are potentially related to climate change. These issues are ultimately met by a community of beekeepers that survives the practice of beekeeping on Gozo through the exchange of local knowledge and dialogue. I left Gozo with further questions about how the islet’s environment shapes beekeeping and what the future of this practice will look like given our warming planet.
Non-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, develo... more Non-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant–microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20–22 nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences, with about half of them encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and xisRNA loci predominantly coincide w...
ABSTRACTNon-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth... more ABSTRACTNon-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant-microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20-22nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences often encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and some xisRNA loci coincide with the coding sequen...
Uploads
Papers by Florence Auguy