Salvia miltiorrhiza is well known for its clinical practice in treating heart and cardiovascular diseases.Its roots,used for traditional Chinese medicine materials,are usually brick-red due to accumulation of red pigm...Salvia miltiorrhiza is well known for its clinical practice in treating heart and cardiovascular diseases.Its roots,used for traditional Chinese medicine materials,are usually brick-red due to accumulation of red pigments,such as tanshinone IIA and tanshinone I.Here we report a S.miltiorrhiza line(shh)with orange roots.Compared with the red roots of normal S.miltiorrhiza plants,the contents of tanshinones with a single bond at C-15,16 were increased,whereas those with a double bond at C-15,16 were significantly decreased in shh.We assembled a high-quality chromosome-level genome of shh.Phylogenomic analysis showed that the relationship between two S.miltiorrhiza lines with red roots was closer than the relationship with shh.It indicates that shh could not be the mutant of an extant S.miltiorrhiza line with red roots.Comparative genomic and transcriptomic analyses showed that a 1.0 kb DNA fragment was deleted in shh Sm2OGD3m.Complementation assay showed that overexpression of intact Sm2OGD3 in shh hairy roots recovered furan D-ring tanshinone accumulation.Consistently,in vitro protein assay showed that Sm2OGD3 catalyzed the conversion of cyptotanshinone,15,16-dihydrotanshinone I and 1,2,15,16-tetrahydrotanshinone I into tanshinone IIA,tanshinone I and 1,2-dihydrotanshinone I,respectively.Thus,Sm2OGD3 functions as tanshinone 15,16-dehydrogenase and is a key enzyme in tanshinone biosynthesis.The results provide novel insights into the metabolic network of medicinally important tanshinone compounds.展开更多
Salvia miltiorrhiza is a model medicinal plant with significant economic and medicinal value.Its roots produce a group of diterpenoid lipophilic bioactive components,termed tanshinones.Biosynthesis and regulation of t...Salvia miltiorrhiza is a model medicinal plant with significant economic and medicinal value.Its roots produce a group of diterpenoid lipophilic bioactive components,termed tanshinones.Biosynthesis and regulation of tanshinones has attracted widespread interest.However,the methylome of S.miltiorrhiza has not been analysed and the regulatory mechanism of DNA methylation in tanshinone production is largely unknown.Here we report single-base resolution DNA methylomes from roots and leaves.Comparative analysis revealed differential methylation patterns for CG,CHG,and CHH contexts and the association between DNA methylation and the expression of genes and small RNAs.Lowly methylated genes always had higher expression levels and 24-nucleotide sRNAs could be key players in the RdDM pathway in S.miltiorrhiza.DNA methylation variation analysis showed that CHH methylation contributed mostly to the difference.Go enrichment analysis showed that diterpenoid biosynthetic process was significantly enriched for genes with downstream overlapping with hypoCHHDMR in July_root when comparing with those in March_root.Tanshinone biosynthesis-related enzyme genes,such as DXS2,CMK,IDI1,HMGR2,DXR,MDS,CYP76AH1,2OGD25,and CYP71D373,were less CHH methylated in gene promoters or downstream regions in roots collected in July than those collected in March.Consistently,gene expression was up-regulated in S.miltiorrhiza roots collected in July compared with March and the treatment of DNA methylation inhibitor 5-azacytidine significantly promoted tanshinone production.It suggests that DNA methylation plays a significant regulatory role in tanshinone biosynthesis in S.miltiorrhiza through changing the levels of CHH methylation in promoters or downstreams of key enzyme genes.展开更多
Plants develop important regulatory networks to adapt to the frequently-changing availability of copper （Cu）, However, little is known about miRNA-associated Cu-regulatory networks in plant species other than Arabid...Plants develop important regulatory networks to adapt to the frequently-changing availability of copper （Cu）, However, little is known about miRNA-associated Cu-regulatory networks in plant species other than Arabidopsis. Here, we report that Cu-responsive miRNAs in Populus trichocarpa （Torr. ＆ Gray） include not only conserved miR397, miR398 and miR408, but also Populus-specific miR1444, suggesting the conservation and diversity of Cu-responsive miRNAs in plants. Copper-associated suppression of mature miRNAs is in company with the up-regulation of their target genes encoding Cu-containing proteins in Populus. The targets include miR397-targeted PtLAC5, PtLAC6 and PtLAC110a, miR398- targeted PtCSD1, PtCSD2a and PtCSD2b, miR408-targeted PtPCL1, PtPCL2, PtPCL3 and PtLAC4, and miR1444-targeted PtPP03 and PtPP06. Consistently, P. trichocarpa miR408 promoter-directed GUS gene expression is down-regulated by Cu in transgenic tobacco plants. Cu-response elements （CuREs） are found in the promoters of Cu-responsive miRNA genes. We identified 34 SQUAMOSA-promoter binding protein-like （SPL） genes, of which 17 are full-length PtSPL proteins or partial sequences with at least 300 amino acids. Phylogenetic analysis indicates that PtSPL3 and PtSPL4 are CuRE-binding proteins controlling Cu-responsive gene expression. Cu appears to be not involved in the regulation of these transcription factors because neither PtSPL3 nor PtSPL4 is Cu-regulated and no CuRE exists in their promoters.展开更多
Dear Editor,The regulatory role of herbal s RNAs in humans and animals is an interesting research topic.However,current evidence is insufficient to conclude that herbal sRNAs are novel precision medicines.I previously...Dear Editor,The regulatory role of herbal s RNAs in humans and animals is an interesting research topic.However,current evidence is insufficient to conclude that herbal sRNAs are novel precision medicines.I previously showed that HJT-s RNA-m1-HJT-s RNA-m8,identified as herbal sRNAs previously(Du et al.,2019),may be derived from humans and/or animals(Lu,2023).展开更多
SQUAMOSA promoter binding protein-likes （SPLs） are plant-specific transcription factors playing vital regulatory roles in plant growth and development. There is no information about SPLs in Salvia miltiorrhiza （Dan...SQUAMOSA promoter binding protein-likes （SPLs） are plant-specific transcription factors playing vital regulatory roles in plant growth and development. There is no information about SPLs in Salvia miltiorrhiza （Danshen）, a significant medicinal plant widely used in Traditional Chinese medicine （TCM） for＆gt;1,700 years and an emerging model plant for TCM studies. Through genome-wide identification and subsequent molecular cloning, we identified a total 15 SmSPLs with divergent sequence features, gene structures, and motifs. Comparative analysis showed sequence conservation between SmSPLs and their Arabidopsis counterparts. A phylogenetic tree clusters SmSPLs into six groups. Many of the motifs identified commonly exist in a group/subgroup, implying their functional redundancy. Eight SmSPLs were predicted and experimental y validated to be targets of miR156/157. SmSPLs were differen-tial y expressed in various tissues of S. milltiorrhiza. The expression of miR156/157-targeted SmSPLs was increased with＆amp;nbsp;the maturation of S. miltiorrhiza, whereas the expression of miR156/157 was decreased, confirming the regulatory roles of miR156/157 in SmSPLs and suggesting the functions of SmSPLs in S. miltiorrhiza development. The expression of miR156/157 was negatively correlated with miR172 during the maturation of S. miltiorrhiza. The results indicate the significance and complexity of SmSPL-, miR156-, and miR172-mediated regula-tion of developmental timing in S. miltiorrhiza.展开更多
Development of the graft union of explanted internode autografting of cucumber ( Cu-cumis sativus Linn.) cultured in vitro is regulated by plant hormones exogenously added to the media. The levels of auxin (indole-3-a...Development of the graft union of explanted internode autografting of cucumber ( Cu-cumis sativus Linn.) cultured in vitro is regulated by plant hormones exogenously added to the media. The levels of auxin (indole-3-acetic acid, IAA) and zeatin plus zeatin riboside (Z+ ZR) in graft unions and in 4 parts of the graft union have been analyzed by ELISA assay.展开更多
Increasing evidence suggests that long non-coding RNAs（lnc RNAs） play significant roles in plants.However,little is known about lnc RNAs in Panax ginseng C.A.Meyer,an economically significant medicinal plant species...Increasing evidence suggests that long non-coding RNAs（lnc RNAs） play significant roles in plants.However,little is known about lnc RNAs in Panax ginseng C.A.Meyer,an economically significant medicinal plant species.A total of3,688 m RNA-like non-coding RNAs（mlnc RNAs）,a class of lnc RNAs,were identified in P.ginseng.Approximately 40% of the identified mlnc RNAs were processed into small RNAs,implying their regulatory roles via small RNA-mediated mechanisms.Eleven mi RNA-generating mlnc RNAs also produced si RNAs,suggesting the coordinated production of mi RNAs and si RNAs in P.ginseng.The mlnc RNA-derived small RNAs might be 21-,22-,or 24-nt phased and could be generated from both or only one strand of mlnc RNAs,or from super long hairpin structures.A full-length mlnc RNA,termed MAR（multiple-function-associated mlnc RNA）,was cloned.It generated the most abundant si RNAs.The MAR si RNAs were Researchpredominantly 24-nt and some of them were distributed in a phased pattern.A total of 228 targets were predicted for 71 MAR si RNAs.Degradome sequencing validated 68 predicted targets involved in diverse metabolic pathways,suggesting the significance of MAR in P.ginseng.Consistently,MAR was detected in all tissues analyzed and responded to methyl jasmonate（Me JA） treatment.It sheds light on the function of mlncRNAs in plants.展开更多
Dear Editor,In 2012,Zhang et al.(2012)published an interesting and widely cited article in Cell Research.They reported that exogenous plant miR168a could enter mammals through oral food intake to regulate the expressi...Dear Editor,In 2012,Zhang et al.(2012)published an interesting and widely cited article in Cell Research.They reported that exogenous plant miR168a could enter mammals through oral food intake to regulate the expression of mammalian LDLRAP1 gene.From then on,cross-kingdom regulation of diet-derived plant miRNAs has generated substantial interest and attracted media to report.Although there is evidence to support this point of view,the authenticity of cross-kingdom regulation of plant miRNAs has been widely questioned.In 2019,Science China Life Sciences published a special topic entitled“Herbal small RNA,novel precision medicine from Mother Nature”,in which the authors tried to demonstrate an idea that herbal sRNAs are novel precision medicines.This is a thought further than cross-kingdom regulation of sRNAs.However,are herbal sRNAs really novel precision medicines?展开更多
MicroRNAs are a class of endogenous small non-coding RNAs,some of which can trigger phased secondary small interfering RNA(phasiRNA)production from target genes.Mitochondrial transcription termination factors(mTERFs),...MicroRNAs are a class of endogenous small non-coding RNAs,some of which can trigger phased secondary small interfering RNA(phasiRNA)production from target genes.Mitochondrial transcription termination factors(mTERFs),mainly localized in chloroplasts and/or mitochondria,play critical roles in plant development and stress responses.We report here the identification of 63 mTERFs and a 22 nt novel miRNA(smi-miRmTERF),which directly cleave SmmTERF33 and SmmTERF45 transcripts to trigger phasiRNA biogenesis.The generated phasiRNAs could further trigger phasiRNA biogenesis from SmmTERF26 and regulated a subset of lineage-specific SmmTERFs.MIRmTERF widely existed in Nepetoideae plants and SmmTERF33 and SmmTERF45 proteins were localized in chloroplasts,mitochondria,and the cytoplasm.Smi-miRmTERF overexpression(MIRMTERF#OE)resulted in a dwarfing phenotype with severe defects in chloroplast and mitochondrial morphogenesis.Transcriptomic analysis showed up-regulation of defenserelated and down-regulation of photosynthesis-related genes in MIRMTERF#OE plants.Under norflurazon and lincomycin treatments,MIRMTERF#OE plants displayed a gun phenotype,indicating the role of smi-miRmTERF in retrograde signaling.Furthermore,MIRMTERF#OE plants showed increased contents of phenolic acids,monoterpenoids,and sesquiterpenoids and reduced susceptibility to pathogenic bacteria Pst DC3000.The results suggest that smimiRmTERF is a significant regulator of chloroplast and mitochondrial development,retrograde signaling,secondary metabolism,and immunity in S.miltiorrhiza.展开更多
基金financial support from the CAMS Innovation Fund for Medical Sciences(CIFMS)(2021-I2M-1-029)the National Natural Science Foundation of China(81773836).
文摘Salvia miltiorrhiza is well known for its clinical practice in treating heart and cardiovascular diseases.Its roots,used for traditional Chinese medicine materials,are usually brick-red due to accumulation of red pigments,such as tanshinone IIA and tanshinone I.Here we report a S.miltiorrhiza line(shh)with orange roots.Compared with the red roots of normal S.miltiorrhiza plants,the contents of tanshinones with a single bond at C-15,16 were increased,whereas those with a double bond at C-15,16 were significantly decreased in shh.We assembled a high-quality chromosome-level genome of shh.Phylogenomic analysis showed that the relationship between two S.miltiorrhiza lines with red roots was closer than the relationship with shh.It indicates that shh could not be the mutant of an extant S.miltiorrhiza line with red roots.Comparative genomic and transcriptomic analyses showed that a 1.0 kb DNA fragment was deleted in shh Sm2OGD3m.Complementation assay showed that overexpression of intact Sm2OGD3 in shh hairy roots recovered furan D-ring tanshinone accumulation.Consistently,in vitro protein assay showed that Sm2OGD3 catalyzed the conversion of cyptotanshinone,15,16-dihydrotanshinone I and 1,2,15,16-tetrahydrotanshinone I into tanshinone IIA,tanshinone I and 1,2-dihydrotanshinone I,respectively.Thus,Sm2OGD3 functions as tanshinone 15,16-dehydrogenase and is a key enzyme in tanshinone biosynthesis.The results provide novel insights into the metabolic network of medicinally important tanshinone compounds.
基金This work was supported by the CAMS Innovation Fund for Medi-cal Sciences(CIFMS)(2021-I2M-2-001).
文摘Salvia miltiorrhiza is a model medicinal plant with significant economic and medicinal value.Its roots produce a group of diterpenoid lipophilic bioactive components,termed tanshinones.Biosynthesis and regulation of tanshinones has attracted widespread interest.However,the methylome of S.miltiorrhiza has not been analysed and the regulatory mechanism of DNA methylation in tanshinone production is largely unknown.Here we report single-base resolution DNA methylomes from roots and leaves.Comparative analysis revealed differential methylation patterns for CG,CHG,and CHH contexts and the association between DNA methylation and the expression of genes and small RNAs.Lowly methylated genes always had higher expression levels and 24-nucleotide sRNAs could be key players in the RdDM pathway in S.miltiorrhiza.DNA methylation variation analysis showed that CHH methylation contributed mostly to the difference.Go enrichment analysis showed that diterpenoid biosynthetic process was significantly enriched for genes with downstream overlapping with hypoCHHDMR in July_root when comparing with those in March_root.Tanshinone biosynthesis-related enzyme genes,such as DXS2,CMK,IDI1,HMGR2,DXR,MDS,CYP76AH1,2OGD25,and CYP71D373,were less CHH methylated in gene promoters or downstream regions in roots collected in July than those collected in March.Consistently,gene expression was up-regulated in S.miltiorrhiza roots collected in July compared with March and the treatment of DNA methylation inhibitor 5-azacytidine significantly promoted tanshinone production.It suggests that DNA methylation plays a significant regulatory role in tanshinone biosynthesis in S.miltiorrhiza through changing the levels of CHH methylation in promoters or downstreams of key enzyme genes.
基金supported by the Forest Biotech-nology Industrial Research Consortium at North Carolina State University, USAthe National High-Tech Research and Development Program (863 Program) of China (2009AA10Z101)+1 种基金the National Natural Science Foundation of China (31070534)the Program for Xiehe Scholars in the Chinese Academy of Medical Sciences & Peking Union Medical College
文摘Plants develop important regulatory networks to adapt to the frequently-changing availability of copper （Cu）, However, little is known about miRNA-associated Cu-regulatory networks in plant species other than Arabidopsis. Here, we report that Cu-responsive miRNAs in Populus trichocarpa （Torr. ＆ Gray） include not only conserved miR397, miR398 and miR408, but also Populus-specific miR1444, suggesting the conservation and diversity of Cu-responsive miRNAs in plants. Copper-associated suppression of mature miRNAs is in company with the up-regulation of their target genes encoding Cu-containing proteins in Populus. The targets include miR397-targeted PtLAC5, PtLAC6 and PtLAC110a, miR398- targeted PtCSD1, PtCSD2a and PtCSD2b, miR408-targeted PtPCL1, PtPCL2, PtPCL3 and PtLAC4, and miR1444-targeted PtPP03 and PtPP06. Consistently, P. trichocarpa miR408 promoter-directed GUS gene expression is down-regulated by Cu in transgenic tobacco plants. Cu-response elements （CuREs） are found in the promoters of Cu-responsive miRNA genes. We identified 34 SQUAMOSA-promoter binding protein-like （SPL） genes, of which 17 are full-length PtSPL proteins or partial sequences with at least 300 amino acids. Phylogenetic analysis indicates that PtSPL3 and PtSPL4 are CuRE-binding proteins controlling Cu-responsive gene expression. Cu appears to be not involved in the regulation of these transcription factors because neither PtSPL3 nor PtSPL4 is Cu-regulated and no CuRE exists in their promoters.
文摘Dear Editor,The regulatory role of herbal s RNAs in humans and animals is an interesting research topic.However,current evidence is insufficient to conclude that herbal sRNAs are novel precision medicines.I previously showed that HJT-s RNA-m1-HJT-s RNA-m8,identified as herbal sRNAs previously(Du et al.,2019),may be derived from humans and/or animals(Lu,2023).
基金supported by grants from the Beijing Natural Science Foundation(Grant No.5112026 to S.L.)the Major Scientific and Technological Special Project for Significant New Drugs Creation(Grant No.2012ZX09301002-001-031 to S.L.)+2 种基金the Research Fund for the Doctoral Program of Higher Education of China(20111106110033 to S.L.)the Program for Changjiang Scholars and Innovative Research Team in University(PCSIRT,Grant No.IRT1150)the Program for Xiehe Scholars in Chinese Academy of Medical Sciences&Peking Union Medical College(to S.L.)
文摘SQUAMOSA promoter binding protein-likes （SPLs） are plant-specific transcription factors playing vital regulatory roles in plant growth and development. There is no information about SPLs in Salvia miltiorrhiza （Danshen）, a significant medicinal plant widely used in Traditional Chinese medicine （TCM） for＆gt;1,700 years and an emerging model plant for TCM studies. Through genome-wide identification and subsequent molecular cloning, we identified a total 15 SmSPLs with divergent sequence features, gene structures, and motifs. Comparative analysis showed sequence conservation between SmSPLs and their Arabidopsis counterparts. A phylogenetic tree clusters SmSPLs into six groups. Many of the motifs identified commonly exist in a group/subgroup, implying their functional redundancy. Eight SmSPLs were predicted and experimental y validated to be targets of miR156/157. SmSPLs were differen-tial y expressed in various tissues of S. milltiorrhiza. The expression of miR156/157-targeted SmSPLs was increased with＆amp;nbsp;the maturation of S. miltiorrhiza, whereas the expression of miR156/157 was decreased, confirming the regulatory roles of miR156/157 in SmSPLs and suggesting the functions of SmSPLs in S. miltiorrhiza development. The expression of miR156/157 was negatively correlated with miR172 during the maturation of S. miltiorrhiza. The results indicate the significance and complexity of SmSPL-, miR156-, and miR172-mediated regula-tion of developmental timing in S. miltiorrhiza.
文摘Development of the graft union of explanted internode autografting of cucumber ( Cu-cumis sativus Linn.) cultured in vitro is regulated by plant hormones exogenously added to the media. The levels of auxin (indole-3-acetic acid, IAA) and zeatin plus zeatin riboside (Z+ ZR) in graft unions and in 4 parts of the graft union have been analyzed by ELISA assay.
基金supported by the Natural Science Foundation of China (31200197 and 81072993)the Major Scientific and Technological Special Project for Significant New Drugs Creation (2012ZX09301002-001-031)+3 种基金the Program for Changjiang Scholars and Innovative Research Team in University (PCSIRT,IRT1150)the Program for Xiehe Scholars in Chinese Academy of Medical Sciences and Peking Union Medical College (to S.L.)the Scientific Research Foundation for Returned Oversea Chinese Scholars,Human Resources and Social Security Department of China (to S.L.)the Program for Xiehe Scholars and Innovative Research Team in Chinese Academy of Medical Sciences (YKRBH(2011)26)
文摘Increasing evidence suggests that long non-coding RNAs（lnc RNAs） play significant roles in plants.However,little is known about lnc RNAs in Panax ginseng C.A.Meyer,an economically significant medicinal plant species.A total of3,688 m RNA-like non-coding RNAs（mlnc RNAs）,a class of lnc RNAs,were identified in P.ginseng.Approximately 40% of the identified mlnc RNAs were processed into small RNAs,implying their regulatory roles via small RNA-mediated mechanisms.Eleven mi RNA-generating mlnc RNAs also produced si RNAs,suggesting the coordinated production of mi RNAs and si RNAs in P.ginseng.The mlnc RNA-derived small RNAs might be 21-,22-,or 24-nt phased and could be generated from both or only one strand of mlnc RNAs,or from super long hairpin structures.A full-length mlnc RNA,termed MAR（multiple-function-associated mlnc RNA）,was cloned.It generated the most abundant si RNAs.The MAR si RNAs were Researchpredominantly 24-nt and some of them were distributed in a phased pattern.A total of 228 targets were predicted for 71 MAR si RNAs.Degradome sequencing validated 68 predicted targets involved in diverse metabolic pathways,suggesting the significance of MAR in P.ginseng.Consistently,MAR was detected in all tissues analyzed and responded to methyl jasmonate（Me JA） treatment.It sheds light on the function of mlncRNAs in plants.
文摘Dear Editor,In 2012,Zhang et al.(2012)published an interesting and widely cited article in Cell Research.They reported that exogenous plant miR168a could enter mammals through oral food intake to regulate the expression of mammalian LDLRAP1 gene.From then on,cross-kingdom regulation of diet-derived plant miRNAs has generated substantial interest and attracted media to report.Although there is evidence to support this point of view,the authenticity of cross-kingdom regulation of plant miRNAs has been widely questioned.In 2019,Science China Life Sciences published a special topic entitled“Herbal small RNA,novel precision medicine from Mother Nature”,in which the authors tried to demonstrate an idea that herbal sRNAs are novel precision medicines.This is a thought further than cross-kingdom regulation of sRNAs.However,are herbal sRNAs really novel precision medicines?
基金supported by the CAMS Innovation Fund for Medical Sciences(CIFMS)(2022-I2M-2–001).
文摘MicroRNAs are a class of endogenous small non-coding RNAs,some of which can trigger phased secondary small interfering RNA(phasiRNA)production from target genes.Mitochondrial transcription termination factors(mTERFs),mainly localized in chloroplasts and/or mitochondria,play critical roles in plant development and stress responses.We report here the identification of 63 mTERFs and a 22 nt novel miRNA(smi-miRmTERF),which directly cleave SmmTERF33 and SmmTERF45 transcripts to trigger phasiRNA biogenesis.The generated phasiRNAs could further trigger phasiRNA biogenesis from SmmTERF26 and regulated a subset of lineage-specific SmmTERFs.MIRmTERF widely existed in Nepetoideae plants and SmmTERF33 and SmmTERF45 proteins were localized in chloroplasts,mitochondria,and the cytoplasm.Smi-miRmTERF overexpression(MIRMTERF#OE)resulted in a dwarfing phenotype with severe defects in chloroplast and mitochondrial morphogenesis.Transcriptomic analysis showed up-regulation of defenserelated and down-regulation of photosynthesis-related genes in MIRMTERF#OE plants.Under norflurazon and lincomycin treatments,MIRMTERF#OE plants displayed a gun phenotype,indicating the role of smi-miRmTERF in retrograde signaling.Furthermore,MIRMTERF#OE plants showed increased contents of phenolic acids,monoterpenoids,and sesquiterpenoids and reduced susceptibility to pathogenic bacteria Pst DC3000.The results suggest that smimiRmTERF is a significant regulator of chloroplast and mitochondrial development,retrograde signaling,secondary metabolism,and immunity in S.miltiorrhiza.
