Proteins usually assemble oligomers or high-order complexes to increase their efficiency and specificity in biological processes.The dynamic equilibrium of complex formation and disruption imposes reversible regulatio...Proteins usually assemble oligomers or high-order complexes to increase their efficiency and specificity in biological processes.The dynamic equilibrium of complex formation and disruption imposes reversible regulation of protein function.MicroProteins are small,single-domain proteins that directly bind target protein complexes and disrupt their assembly.Growing evidence shows that microProteins are efficient regulators of protein activity at the post-translational level.In the last few decades,thousands of plant microProteins have been predicted by computational approaches,but only a few have been experimentally validated.Recent studies highlighted the mechanistic working modes of newly-identified microProteins in Arabidopsis and other plant species.Here,we review characterized microProteins,including their biological roles,regulatory targets,and modes of action.In particular,we focus on microProtein-directed allosteric modulation of key components in light signaling pathways,and we summarize the biogenesis and evolutionary trajectory of known microProteins in plants.Understanding the regulatory mechanisms of microProteins is an important step towards potential utilization of microProteins as versatile biotechnological tools in crop bioengineering.展开更多
Reprogramming oncogenic signaling pathways to generate anti-tumor effects is a promising strategy for targeted cancer intervention,without significant off-target effects.Although reprogramming multioncoprotein interac...Reprogramming oncogenic signaling pathways to generate anti-tumor effects is a promising strategy for targeted cancer intervention,without significant off-target effects.Although reprogramming multioncoprotein interactions in a single signaling pathway axis has been shown to achieve sustained efficacy,there are several challenges that limit its clinical application.Herein,we transformed the mouse double minute 2 homolog(MDM2)-heat shock cognate protein 70(HSC70)axis,a tumor-promoting pathway,into an activator of anti-tumor immunity using the Path-editor,an artificial selenoprotein.Once it enters the cell,Path-editor decomposes into PMI and PPI peptides:PMI inhibits MDM2-mediated p53 degradation and promotes HSC70 expression,while PPI binds to HSC70,enabling its ability to selectively degrade the programmed cell death ligand 1(PD-L1).As a proof of concept,we tested its performance in microsatellite-stable(MSS)colorectal cancer,which typically displays limited responsiveness to immunotherapy.The results indicated that Path-editor effectively attenuated PD-L1 expression and reversed immune evasion in both CT26 allografts and humanized patient-derived tumor xenograft(PDX)models,thereby inhibiting tumor progression with high biosafety.Therefore,this paper introduces Path-editor as a paradigm for reprogramming oncogenic multi-protein pathways,utilizing selenium-assisted approach to achieve the rapid design of tumor-specific pathway editors.This strategy is expected to reverse immune escape in MSS colorectal cancer and treat difficult malignancies.展开更多
Objective:To analyze the different clinical features of patients with early-onset(EO-NMOSDs)and late-onset neuromyelitis optica spectrum diseases(LO-NMOSDs).Methods:A total of 51patients with neuromyelitis optica spec...Objective:To analyze the different clinical features of patients with early-onset(EO-NMOSDs)and late-onset neuromyelitis optica spectrum diseases(LO-NMOSDs).Methods:A total of 51patients with neuromyelitis optica spectrum disease who were diagnosed in our hospital for the first time from January 2015 to December 2022 were included in the First Affiliated Hospital of Hainan Medical College and divided into 22 cases in the EO-NMOSDs group and 29 cases in the LO-NMOSDs group according to whether the age of onset was 50 years old.The basic data,Extended Disability Status Scale(EDSS)score,blood and cerebrospinal fluid test indicators of the two groups were statistically analyzed.Results:There were no significant differences in demographic characteristics,clinical features and serum AQP-4 antibody positivity rate between the two groups(all P>0.05),and there were significant differences in triglycerides(TG),low-density lipoprotein(LDL),apolipoprotein A(APOA),apolipoprotein B(APOB)and lipoprotein a(P=0.010,P=0.048,P=0.014,P=0.061,P=0.001,respectively),and cerebrospinal fluid LDH,There were significant differences between microprotein quantification and EDSS score(P=0.018,P=0.034,P=0.025,respectively),and the level of microprotein quantification in cerebrospinal fluid of LO-NMOSDs had a certain correlation with the degree of disability(r=0.52,P<0.03).Conclusion:LO-NMOSDs and EO-NMOSDs group patients have similar demographic characteristics,serum AQP-4 antibody positive rate and clinical features,but compared with EO-NMOSDs,patients in LO-NMOSDs group are prone to abnormal lipid metabolism,higher trace proteins in cerebrospinal fluid and more likely to be disabled,and among LO-NMOSDs,the higher the trace protein in the cerebrospinal fluid,the more severe the disability status of patients.展开更多
A substantial but largely unexplored fraction of eukaryotic proteomes is composed of peptides and small proteins(the peptidome).In recent years,short open reading frames(sORFs)capable of encoding functional peptides h...A substantial but largely unexplored fraction of eukaryotic proteomes is composed of peptides and small proteins(the peptidome).In recent years,short open reading frames(sORFs)capable of encoding functional peptides have been identified within transcripts annotated as non-coding RNAs or in intergenic regions.These sORF-encoded peptides(SEPs)were previously overlooked due to their small size and difficulties in detection,both experimentally and computationally.However,analyses of translating RNAs(ribosome profiling)and proteomics(mass spectrometry)have provided growing evidence for the existence of numerous novel‘non-conventional’peptides in eukaryotic organisms,including plants.In animals,mounting evidence indicates that long non-coding RNAs are an important source of SEPs,and that SEPs participate in crucial cellular and physiological processes and can mediate the evolution of novel characteristics.Similar findings are now emerging in plants.The SEP-coding capacity and the full repertoire of functional SEPs within eukaryotic genomes remain unclear,but systematic,large-scale molecular screenings are beginning to address this gap.Here,we review current progress in understanding the plant non-conventional peptidome,explore parallels between plants and animals,and illustrate how findings in animals can help guide plant research on this topic.展开更多
Emerging evidence demonstrates that cryptic translation from RNAs previously annotated as noncoding might generate microproteins with oncogenic functions.However,the importance and underlying mechanisms of these micro...Emerging evidence demonstrates that cryptic translation from RNAs previously annotated as noncoding might generate microproteins with oncogenic functions.However,the importance and underlying mechanisms of these microproteins in alternative splicing-driven tumor progression have rarely been studied.Here,we show that the novel protein TPM3P9,encoded by the lncRNA tropomyosin 3 pseudogene 9,exhibits oncogenic activity in clear cell renal cell carcinoma(ccRCC)by enhancing oncogenic RNA splicing.Overexpression of TPM3P9 promotes cell proliferation and tumor growth.Mechanistically,TPM3P9 binds to the RRM1 domain of the splicing factor RBM4 to inhibit RBM4-mediated exon skipping in the transcription factor TCF7L2.This results in increased expression of the oncogenic splice variant TCF7L2-L,which activates NF-κB signaling via its interaction with SAM68 to transcriptionally induce RELB expression.From a clinical perspective,TPM3P9 expression is upregulated in cancer tissues and is significantly correlated with the expression of TCF7L2-L and RELB.High TPM3P9 expression or low RBM4 expression is associated with poor survival in patients with ccRCC.Collectively,our findings functionally and clinically characterize the“noncoding RNA”-derived microprotein TPM3P9 and thus identify potential prognostic and therapeutic factors in renal cancer.展开更多
Stress and illness connection is complex and involves multiple physiological systems.Panax ginsengs,reputed for their broad-spectrum“cure-all”effect,are widely prescribed to treat stress and related illnesses.Howeve...Stress and illness connection is complex and involves multiple physiological systems.Panax ginsengs,reputed for their broad-spectrum“cure-all”effect,are widely prescribed to treat stress and related illnesses.However,the identity of ginseng’s“cure-all”medicinal compounds that relieve stress remains unresolved.Here,we identify ginsentides as the principal bioactives that coordinate multiple systems to restore homeostasis in response to stress.Ginsentides are disulfide-rich,cell-penetrating and proteolytic-stable microproteins.Using affinity-enrichment mass spectrometry target identification together with in vitro,ex vivo and in vivo validations,we show that highly purified or synthetic ginsentides promote vasorelaxation by producing nitric oxide through endothelial cells via intracellular PI3K/Akt signaling pathway,alleviate a1-adrenergic receptor overactivity by reversing phenylephrine-induced constriction of aorta,decrease monocyte adhesion to endothelial cells via CD166/ESAM/CD40 and inhibit P2Y12 receptors to reduce platelet aggregation.Orally administered ginsentides were effective in animal models to reduce ADP-induced platelet aggregation,to prevent collagen and adrenalineinduced pulmonary thrombosis as well as anti-stress behavior of tail suspension and forced swimming tests in mice.Together,these results strongly suggest that ginsentides are the principal panacea compounds of ginsengs because of their ability to target multiple extra-and intra-cellular proteins to reverse stress-induced damages.展开更多
The roles of concealed microproteins encoded by long noncoding RNAs(lncRNAs)are gradually being exposed,but their functions in tumorigenesis are still largely unclear.Here,we identify and characterize a conserved 99-a...The roles of concealed microproteins encoded by long noncoding RNAs(lncRNAs)are gradually being exposed,but their functions in tumorigenesis are still largely unclear.Here,we identify and characterize a conserved 99-amino acid microprotein named KRASIM that is encoded by the putative lncRNA NCBP2-AS2.KRASIM is differentially expressed in normal hepatocytes and hepatocellular carcinoma(HCC)cells and can suppress HCC cell growth and proliferation.Mechanistically,KRASIM interacts and colocalizes with the KRAS protein in the cytoplasm of human HuH-7 hepatoma cells.More importantly,the overexpression of KRASIM decreases the KRAS protein level,leading to the inhibition of ERK signaling activity in HCC cells.These results demonstrate a novel microprotein repressor of the KRAS pathway for the first time and provide new insights into the regulatory mechanisms of oncogenic signaling and HCC therapy.展开更多
Breeding plants with polyploid genomes is challenging because functional redundancy hampers the identification of loss-of-function mutants.Medicago sativa is tetraploid and obligate outcrossing,which together with inb...Breeding plants with polyploid genomes is challenging because functional redundancy hampers the identification of loss-of-function mutants.Medicago sativa is tetraploid and obligate outcrossing,which together with inbreeding depression complicates traditional breeding approaches in obtaining plants with a stable growth habit.Inducing dominant mutations would provide an alternative strategy to introduce domestication traits in plants with high gene redundancy.Here we describe two complementary strategies to induce dominant mutations in the M.sativa genome and how they can be relevant in the control of flowering time.First,we outline a genome-engineering strategy that harnesses the use of microProteins as developmental regulators.MicroProteins are small proteins that appeared during genome evolution from genes encoding larger proteins.Genomeengineering allows us to retrace evolution and create microProtein-coding genes de novo.Second,we provide an inventory of genes regulated by microRNAs that control plant development.Making respective gene transcripts microRNA-resistant by inducing point mutations can uncouple microRNA regulation.Finally,we investigated the recently published genomes of M.sativa and provide an inventory of breeding targets,some of which,when mutated,are likely to result in dominant traits.展开更多
基金supported by the National Natural Science Foundation of China(31770208)the Support Project of High-Level Teachers in Beijing Municipal Universities in the Period of 13th Five-Year Plan(CIT&TCD20190331).
文摘Proteins usually assemble oligomers or high-order complexes to increase their efficiency and specificity in biological processes.The dynamic equilibrium of complex formation and disruption imposes reversible regulation of protein function.MicroProteins are small,single-domain proteins that directly bind target protein complexes and disrupt their assembly.Growing evidence shows that microProteins are efficient regulators of protein activity at the post-translational level.In the last few decades,thousands of plant microProteins have been predicted by computational approaches,but only a few have been experimentally validated.Recent studies highlighted the mechanistic working modes of newly-identified microProteins in Arabidopsis and other plant species.Here,we review characterized microProteins,including their biological roles,regulatory targets,and modes of action.In particular,we focus on microProtein-directed allosteric modulation of key components in light signaling pathways,and we summarize the biogenesis and evolutionary trajectory of known microProteins in plants.Understanding the regulatory mechanisms of microProteins is an important step towards potential utilization of microProteins as versatile biotechnological tools in crop bioengineering.
基金supported by the National Natural Science Foundation of China(Grant No.:82272782)the Shaanxi Natural Science Foundation Research Program,China(Grant No.:2024JCYBMS-795).
文摘Reprogramming oncogenic signaling pathways to generate anti-tumor effects is a promising strategy for targeted cancer intervention,without significant off-target effects.Although reprogramming multioncoprotein interactions in a single signaling pathway axis has been shown to achieve sustained efficacy,there are several challenges that limit its clinical application.Herein,we transformed the mouse double minute 2 homolog(MDM2)-heat shock cognate protein 70(HSC70)axis,a tumor-promoting pathway,into an activator of anti-tumor immunity using the Path-editor,an artificial selenoprotein.Once it enters the cell,Path-editor decomposes into PMI and PPI peptides:PMI inhibits MDM2-mediated p53 degradation and promotes HSC70 expression,while PPI binds to HSC70,enabling its ability to selectively degrade the programmed cell death ligand 1(PD-L1).As a proof of concept,we tested its performance in microsatellite-stable(MSS)colorectal cancer,which typically displays limited responsiveness to immunotherapy.The results indicated that Path-editor effectively attenuated PD-L1 expression and reversed immune evasion in both CT26 allografts and humanized patient-derived tumor xenograft(PDX)models,thereby inhibiting tumor progression with high biosafety.Therefore,this paper introduces Path-editor as a paradigm for reprogramming oncogenic multi-protein pathways,utilizing selenium-assisted approach to achieve the rapid design of tumor-specific pathway editors.This strategy is expected to reverse immune escape in MSS colorectal cancer and treat difficult malignancies.
基金Hainan Clinical Medicine Center Construction Project(2021)Hainan Provincial Excellent Talent Team(QRCBT202121)Key R&D Plan of Hainan Province(ZDYF2022SHFZ109)。
文摘Objective:To analyze the different clinical features of patients with early-onset(EO-NMOSDs)and late-onset neuromyelitis optica spectrum diseases(LO-NMOSDs).Methods:A total of 51patients with neuromyelitis optica spectrum disease who were diagnosed in our hospital for the first time from January 2015 to December 2022 were included in the First Affiliated Hospital of Hainan Medical College and divided into 22 cases in the EO-NMOSDs group and 29 cases in the LO-NMOSDs group according to whether the age of onset was 50 years old.The basic data,Extended Disability Status Scale(EDSS)score,blood and cerebrospinal fluid test indicators of the two groups were statistically analyzed.Results:There were no significant differences in demographic characteristics,clinical features and serum AQP-4 antibody positivity rate between the two groups(all P>0.05),and there were significant differences in triglycerides(TG),low-density lipoprotein(LDL),apolipoprotein A(APOA),apolipoprotein B(APOB)and lipoprotein a(P=0.010,P=0.048,P=0.014,P=0.061,P=0.001,respectively),and cerebrospinal fluid LDH,There were significant differences between microprotein quantification and EDSS score(P=0.018,P=0.034,P=0.025,respectively),and the level of microprotein quantification in cerebrospinal fluid of LO-NMOSDs had a certain correlation with the degree of disability(r=0.52,P<0.03).Conclusion:LO-NMOSDs and EO-NMOSDs group patients have similar demographic characteristics,serum AQP-4 antibody positive rate and clinical features,but compared with EO-NMOSDs,patients in LO-NMOSDs group are prone to abnormal lipid metabolism,higher trace proteins in cerebrospinal fluid and more likely to be disabled,and among LO-NMOSDs,the higher the trace protein in the cerebrospinal fluid,the more severe the disability status of patients.
基金supported by grant PID2022-139578NB-I00(funded by MCIN/AEI/10.13039/501100011033 and by“ERDF A way of making Europe”)and 2021SGR00792(from the Agencia de Gestio d’Ajuts Universitaris i de Recerca)(to J.L.R.)by institutional grants SEV-2015-0533 and CEX2019-000902-S(funded by MCIN/AEI/10.13039/501100011033)+3 种基金by the CERCA Program/Generalitat de Catalunyasupported by fellowship PRE2018-084278funded by MCIN/AEI/10.13039/501100011033by“ESF Investing in your future.”。
文摘A substantial but largely unexplored fraction of eukaryotic proteomes is composed of peptides and small proteins(the peptidome).In recent years,short open reading frames(sORFs)capable of encoding functional peptides have been identified within transcripts annotated as non-coding RNAs or in intergenic regions.These sORF-encoded peptides(SEPs)were previously overlooked due to their small size and difficulties in detection,both experimentally and computationally.However,analyses of translating RNAs(ribosome profiling)and proteomics(mass spectrometry)have provided growing evidence for the existence of numerous novel‘non-conventional’peptides in eukaryotic organisms,including plants.In animals,mounting evidence indicates that long non-coding RNAs are an important source of SEPs,and that SEPs participate in crucial cellular and physiological processes and can mediate the evolution of novel characteristics.Similar findings are now emerging in plants.The SEP-coding capacity and the full repertoire of functional SEPs within eukaryotic genomes remain unclear,but systematic,large-scale molecular screenings are beginning to address this gap.Here,we review current progress in understanding the plant non-conventional peptidome,explore parallels between plants and animals,and illustrate how findings in animals can help guide plant research on this topic.
基金supported by the National Key Research and Development Program of China(2022YFA1304604,2020YFE0202200)the Fundamental Research Funds for the Central Universities(21624109)+3 种基金the Young Scientists Fund of the National Natural Science Foundation of China(82303050)the Guangdong Natural Science Foundation(2022A1515012388)the Natural Science Foundation of Guangdong Province(2023A1515011901)the Guangdong Basic and Applied Basic Research Foundation(2022A1515111106).
文摘Emerging evidence demonstrates that cryptic translation from RNAs previously annotated as noncoding might generate microproteins with oncogenic functions.However,the importance and underlying mechanisms of these microproteins in alternative splicing-driven tumor progression have rarely been studied.Here,we show that the novel protein TPM3P9,encoded by the lncRNA tropomyosin 3 pseudogene 9,exhibits oncogenic activity in clear cell renal cell carcinoma(ccRCC)by enhancing oncogenic RNA splicing.Overexpression of TPM3P9 promotes cell proliferation and tumor growth.Mechanistically,TPM3P9 binds to the RRM1 domain of the splicing factor RBM4 to inhibit RBM4-mediated exon skipping in the transcription factor TCF7L2.This results in increased expression of the oncogenic splice variant TCF7L2-L,which activates NF-κB signaling via its interaction with SAM68 to transcriptionally induce RELB expression.From a clinical perspective,TPM3P9 expression is upregulated in cancer tissues and is significantly correlated with the expression of TCF7L2-L and RELB.High TPM3P9 expression or low RBM4 expression is associated with poor survival in patients with ccRCC.Collectively,our findings functionally and clinically characterize the“noncoding RNA”-derived microprotein TPM3P9 and thus identify potential prognostic and therapeutic factors in renal cancer.
基金supported in part by the Nanyang Technological University Internal Funding-Synzyme and Natural Products(SYNC, Singapore)the AcRF Tier 3 funding (MOE2016-T3-1-003, Singapore)
文摘Stress and illness connection is complex and involves multiple physiological systems.Panax ginsengs,reputed for their broad-spectrum“cure-all”effect,are widely prescribed to treat stress and related illnesses.However,the identity of ginseng’s“cure-all”medicinal compounds that relieve stress remains unresolved.Here,we identify ginsentides as the principal bioactives that coordinate multiple systems to restore homeostasis in response to stress.Ginsentides are disulfide-rich,cell-penetrating and proteolytic-stable microproteins.Using affinity-enrichment mass spectrometry target identification together with in vitro,ex vivo and in vivo validations,we show that highly purified or synthetic ginsentides promote vasorelaxation by producing nitric oxide through endothelial cells via intracellular PI3K/Akt signaling pathway,alleviate a1-adrenergic receptor overactivity by reversing phenylephrine-induced constriction of aorta,decrease monocyte adhesion to endothelial cells via CD166/ESAM/CD40 and inhibit P2Y12 receptors to reduce platelet aggregation.Orally administered ginsentides were effective in animal models to reduce ADP-induced platelet aggregation,to prevent collagen and adrenalineinduced pulmonary thrombosis as well as anti-stress behavior of tail suspension and forced swimming tests in mice.Together,these results strongly suggest that ginsentides are the principal panacea compounds of ginsengs because of their ability to target multiple extra-and intra-cellular proteins to reverse stress-induced damages.
基金This work was supported by the National Key Research and Development Program of China(2017YFA0504400)the National Natural Science Foundation of China(31370791,31671349,31770879)+2 种基金Fundamental Research Funds for the Central Universities(14lgjc18)This research was supported in part by the Guangdong Province Key Laboratory of Computational Science(13lgjc05)the Guangdong Province Computational Science Innovative Research Team(14lgjc18).
文摘The roles of concealed microproteins encoded by long noncoding RNAs(lncRNAs)are gradually being exposed,but their functions in tumorigenesis are still largely unclear.Here,we identify and characterize a conserved 99-amino acid microprotein named KRASIM that is encoded by the putative lncRNA NCBP2-AS2.KRASIM is differentially expressed in normal hepatocytes and hepatocellular carcinoma(HCC)cells and can suppress HCC cell growth and proliferation.Mechanistically,KRASIM interacts and colocalizes with the KRAS protein in the cytoplasm of human HuH-7 hepatoma cells.More importantly,the overexpression of KRASIM decreases the KRAS protein level,leading to the inhibition of ERK signaling activity in HCC cells.These results demonstrate a novel microprotein repressor of the KRAS pathway for the first time and provide new insights into the regulatory mechanisms of oncogenic signaling and HCC therapy.
基金funding through Novo Crops(Novo Nordisk Foundationproject number 2019OC53580+10 种基金S.W.and M.P.)the Independent Research Fund Denmark(0136-00015B and 0135-00014BS.W.)the Novo Nordisk Foundation(NNF18OC0034226 and NNF20OC0061440S.W.)the Innovation Fund Denmark(LESSISMOREM.P.)the Carlsberg Foundation(Raising Quinoaproject number CF181113M.P.)funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sk?odowska Curie grant agreement No.801199(M.J.C.)。
文摘Breeding plants with polyploid genomes is challenging because functional redundancy hampers the identification of loss-of-function mutants.Medicago sativa is tetraploid and obligate outcrossing,which together with inbreeding depression complicates traditional breeding approaches in obtaining plants with a stable growth habit.Inducing dominant mutations would provide an alternative strategy to introduce domestication traits in plants with high gene redundancy.Here we describe two complementary strategies to induce dominant mutations in the M.sativa genome and how they can be relevant in the control of flowering time.First,we outline a genome-engineering strategy that harnesses the use of microProteins as developmental regulators.MicroProteins are small proteins that appeared during genome evolution from genes encoding larger proteins.Genomeengineering allows us to retrace evolution and create microProtein-coding genes de novo.Second,we provide an inventory of genes regulated by microRNAs that control plant development.Making respective gene transcripts microRNA-resistant by inducing point mutations can uncouple microRNA regulation.Finally,we investigated the recently published genomes of M.sativa and provide an inventory of breeding targets,some of which,when mutated,are likely to result in dominant traits.
