Determining how function evolves following gene duplication is necessary for understanding gene expansion.Transcription factors(TFs)are a class of proteins that regulate gene expression by binding to specific cis-acti...Determining how function evolves following gene duplication is necessary for understanding gene expansion.Transcription factors(TFs)are a class of proteins that regulate gene expression by binding to specific cis-acting elements in the promoters of target genes,subsequently activating or repressing their transcription.In the present study,we systematically examined the functional diversification of the NAC transcription factor(NAC-TFs)family by analyzing their chromosomal location,structure,phylogeny,and expression pattern in Gossypium raimondii(Gr)and G.arboreum(Ga).The 145 and 141 NAC genes identified in the Gr and Ga genomes,respectively,were annotated and divided into 18 subfamilies,which showed distinct divergence in gene structure and expression patterns during fiber development.In addition,when the functional parameters were examined,clear divergence was observed within tandem clusters,which suggested that subfunctionalization had occurred among duplicate genes.The expression patterns of homologous gene pairs also changed,suggestive of the diversification of gene function during the evolution of diploid cotton.These findings provide insights into the mechanisms underlying the functional differentiation of duplicated NAC-TFs genes in two diploid cotton species.展开更多
Qingke (Tibetan hulless barley) has long been cultivated and exposed to long-term and strong UV-B radiation on the Tibetan Plateau, which renders it an ideal species for elucidating novel UV-B responsive mechanisms in...Qingke (Tibetan hulless barley) has long been cultivated and exposed to long-term and strong UV-B radiation on the Tibetan Plateau, which renders it an ideal species for elucidating novel UV-B responsive mechanisms in plants. Here we report a comprehensive metabolite profiling and metabolite-based genome-wide association study (mGWAS) using 196 diverse qingke and barley accessions. Our results demonstrated both constitutive and induced accumulation, and common genetic regulation, of metabolites from different branches of the phenylpropanoid pathway that are involved in UV-B protection. A total of 90 significant mGWAS loci for these metabolites were identified in barley-qingke differentiation regions, and a number of high-level metabolite trait alleles were found to be significantly enriched in qingke, suggesting co-selection of various phenylpropanoids. Upon dissecting the entire phenylpropanoid pathway, we identified some key determinants controlling natural variation of phenylpropanoid content, including three novel proteins, a flavone C-pentosyltransferase, a tyramine hydroxycinnamoyl acyltransferase, and a MYB transcription factor. Our study, furthermore, demonstrated co-selection of both constitutive and induced phenylpropanoids for UV-B protection in qingke.展开更多
To introgress the good fiber quality and yield from Gossypium barbadense into a commercial Upland cotton variety, a high‐density simple sequence repeat （SSR） genetic linkage map was developed from a BC1F1 populatio...To introgress the good fiber quality and yield from Gossypium barbadense into a commercial Upland cotton variety, a high‐density simple sequence repeat （SSR） genetic linkage map was developed from a BC1F1 population of Gossypium hirsutum × Gossypium barbadense. The map com-prised 2,292 loci and covered 5115.16 centiMorgan （cM） of the cotton AD genome, with an average marker interval of 2.23 cM. Of the marker order for 1,577 common loci on this new map, 90.36% agrees well with the marker order on the D genome sequence genetic map. Compared with five pub-lished high‐density SSR genetic maps, 53.14% of marker loci were newly discovered in this map. Twenty‐six quantitative trait loci （QTLs） for lint percentage （LP） were identified on nine chromosomes. Nine stable or common QTLs could be used for marker‐assisted selection. Fifty percent of the QTLs were from G. barbadense and increased LP by 1.07%–2.41%. These results indicated that the map could be used for screening chromosome substitution segments from G. barbadense in the Upland cotton background, identifying QTLs or genes from G. barbadense, and further developing the gene pyramiding effect for improving fiber yield and quality.展开更多
As a major component of the viral ribonucleoprotein(vRNP)complex in influenza A virus(IAV),nucleoprotein(NP)interacts with isoforms of importinαfamily members,leading to the import of itself and vRNP complex into the...As a major component of the viral ribonucleoprotein(vRNP)complex in influenza A virus(IAV),nucleoprotein(NP)interacts with isoforms of importinαfamily members,leading to the import of itself and vRNP complex into the nucleus,a process pivotal in the replication cycle of IAV.In this study,we found that BinCARD1,an isoform of Bcl10-interacting protein with CARD(BinCARD),was leveraged by IAV for efficient viral replication.BinCARD1 promoted the nuclear import of the vRNP complex and newly synthesized NP and thus enhanced vRNP complex activity.Moreover,we found that BinCARD1 interacted with NP to promote NP binding to importinα7,an adaptor in the host nuclear import pathway.However,we also found that BinCARD1 promoted RIG-I-mediated innate immune signaling by mediating Lys63-linked polyubiquitination of TRAF3,and that TBK1 appeared to degrade BinCARD1.We showed that BinCARD1 was polyubiquitinated at residue K103 through a Lys63 linkage,which was recognized by the TBK1-p62 axis for autophagic degradation.Overall,our data demonstrate that IAV leverages BinCARD1 as an important host factor that promotes viral replication,and two mechanisms in the host defense system are triggered—innate immune signaling and autophagic degradation—to mitigate the promoting effect of BinCARD1 on the life cycle of IAV.展开更多
Influenza A virus(IAV) commandeers numerous host cellular factors for successful replication. However, very few host factors have been revealed to be involved in the fusion of viral envelope and late endosomal membran...Influenza A virus(IAV) commandeers numerous host cellular factors for successful replication. However, very few host factors have been revealed to be involved in the fusion of viral envelope and late endosomal membranes. In this study, we identified cation-dependent mannose-6-phosphate receptor(M6PR) as a crucial host factor for the replication of IAV. We found that siRNA knockdown of M6PR expression significantly reduced the growth titers of different subtypes of IAV, and that the inhibitory effect of M6PR siRNA treatment on IAV growth was overcome by the complement of exogenously expressed M6PR. When A549 cells were treated with siRNA targeting M6PR,the nuclear accumulation of viral nucleoprotein(NP) was dramatically inhibited at early timepoints post-infection, indicating that M6PR engages in the early stage of the IAV replication cycle. By investigating the role of M6PR in the individual entry and post-entry steps of IAV replication, we found that the downregulation of M6PR expression had no effect on attachment, internalization, early endosome trafficking,or late endosome acidification. However, we found that M6PR expression was critical for the fusion of viral envelope and late endosomal membranes. Of note, M6PR interacted with the hemagglutinin(HA) protein of IAV, and further studies showed that the lumenal domain of M6PR and the ectodomain of HA2 mediated the interaction and directly promoted the fusion of the viral and late endosomal membranes,thereby facilitating IAV replication. Together, our findings highlight the importance of the M6PR–HA interaction in the fusion of viral and late endosomal membranes during IAV replication.展开更多
Aside from antibodies,peptides show great potential as immune checkpoint inhibitors(ICIs)due to several advantages,such as better tumor penetration and lower cost.Lymphocyte-activation gene 3(LAG-3)is an immune checkp...Aside from antibodies,peptides show great potential as immune checkpoint inhibitors(ICIs)due to several advantages,such as better tumor penetration and lower cost.Lymphocyte-activation gene 3(LAG-3)is an immune checkpoint which can induce T cell dysfunction through interaction with its soluble ligand fibrinogen like protein-1(FGL1).Here,we found that LAG-3 expression was higher than programmed cell death protein 1(PD-1)in multiple human cancers by TCGA databases,and successfully identified a LAG-3 binding peptide LFP-6 by phage display bio-panning,which specifically blocks the interaction of LAG-3/FGL1 but not LAG-3/MHC-II.Subsequently,D-amino acids were introduced to substitute the N-and C-terminus of LFP-6 to obtain the proteolysis-resistant peptide LFP-D1,which restores T cell function in vitro and inhibits tumor growth in vivo.Further,a bispecific peptide LFOP targeting both PD-1/PD-L1 and LAG-3/FGL1 was designed by conjugating LFP-D1 with PD-1/PD-L1blocking peptide OPBP-1(8-12),which activates T cell with enhanced proliferation and IFN-γ production.More importantly,LFOP combined with radiotherapy significantly improve the T cell infiltration in tumor and elevate systemic antitumor immune response.In conclusion,we developed a novel peptide blocking LAG-3/FGL1 which can restore T cell function,and the bispecific peptide synergizes with radiotherapy to further enhance the antitumor immune response.展开更多
基金the National High Technology Research and Development Program of China (2013AA102601)the National Natural Science Foundation of China (31471538)
文摘Determining how function evolves following gene duplication is necessary for understanding gene expansion.Transcription factors(TFs)are a class of proteins that regulate gene expression by binding to specific cis-acting elements in the promoters of target genes,subsequently activating or repressing their transcription.In the present study,we systematically examined the functional diversification of the NAC transcription factor(NAC-TFs)family by analyzing their chromosomal location,structure,phylogeny,and expression pattern in Gossypium raimondii(Gr)and G.arboreum(Ga).The 145 and 141 NAC genes identified in the Gr and Ga genomes,respectively,were annotated and divided into 18 subfamilies,which showed distinct divergence in gene structure and expression patterns during fiber development.In addition,when the functional parameters were examined,clear divergence was observed within tandem clusters,which suggested that subfunctionalization had occurred among duplicate genes.The expression patterns of homologous gene pairs also changed,suggestive of the diversification of gene function during the evolution of diploid cotton.These findings provide insights into the mechanisms underlying the functional differentiation of duplicated NAC-TFs genes in two diploid cotton species.
基金This research was supported by the following funding sources:the Tibet Autonomous Region Financial Special Fund 2015CZZX001,2014CZZXQ01,2015ZX001,2017CZZX001/2,and XZNKY-2018-C-021,and the National Key Research Project Fund,China 2018YFD100070 and 2018YFD1000703.
文摘Qingke (Tibetan hulless barley) has long been cultivated and exposed to long-term and strong UV-B radiation on the Tibetan Plateau, which renders it an ideal species for elucidating novel UV-B responsive mechanisms in plants. Here we report a comprehensive metabolite profiling and metabolite-based genome-wide association study (mGWAS) using 196 diverse qingke and barley accessions. Our results demonstrated both constitutive and induced accumulation, and common genetic regulation, of metabolites from different branches of the phenylpropanoid pathway that are involved in UV-B protection. A total of 90 significant mGWAS loci for these metabolites were identified in barley-qingke differentiation regions, and a number of high-level metabolite trait alleles were found to be significantly enriched in qingke, suggesting co-selection of various phenylpropanoids. Upon dissecting the entire phenylpropanoid pathway, we identified some key determinants controlling natural variation of phenylpropanoid content, including three novel proteins, a flavone C-pentosyltransferase, a tyramine hydroxycinnamoyl acyltransferase, and a MYB transcription factor. Our study, furthermore, demonstrated co-selection of both constitutive and induced phenylpropanoids for UV-B protection in qingke.
基金funded by the National Basic Research Program of China (973 Project) (2010CB126000)the National High Technology Research and Development Program of China (2012AA101108)+1 种基金the National Natural Science Foundation of China (31101188)the fund project of Director (SJA1203)
文摘To introgress the good fiber quality and yield from Gossypium barbadense into a commercial Upland cotton variety, a high‐density simple sequence repeat （SSR） genetic linkage map was developed from a BC1F1 population of Gossypium hirsutum × Gossypium barbadense. The map com-prised 2,292 loci and covered 5115.16 centiMorgan （cM） of the cotton AD genome, with an average marker interval of 2.23 cM. Of the marker order for 1,577 common loci on this new map, 90.36% agrees well with the marker order on the D genome sequence genetic map. Compared with five pub-lished high‐density SSR genetic maps, 53.14% of marker loci were newly discovered in this map. Twenty‐six quantitative trait loci （QTLs） for lint percentage （LP） were identified on nine chromosomes. Nine stable or common QTLs could be used for marker‐assisted selection. Fifty percent of the QTLs were from G. barbadense and increased LP by 1.07%–2.41%. These results indicated that the map could be used for screening chromosome substitution segments from G. barbadense in the Upland cotton background, identifying QTLs or genes from G. barbadense, and further developing the gene pyramiding effect for improving fiber yield and quality.
基金This investigation was funded by a grant from the Laboratory of Lingnan Modern Agriculture Project(NT2021007 to HC and CL)the National Natural Science Foundation of China(NSFC)(32192453 to CL,32172847 to LJ)+2 种基金the National Key Research and Development Program of China(2021YFD1800203 to HC,2021YFD1800204 to CL)the Natural Science Foundation of Heilongjiang Province(JQ2019C005 to CL)the Central Public-Interest Scientific Institution Basal Research Fund(Y2017JC35 to GT).
文摘As a major component of the viral ribonucleoprotein(vRNP)complex in influenza A virus(IAV),nucleoprotein(NP)interacts with isoforms of importinαfamily members,leading to the import of itself and vRNP complex into the nucleus,a process pivotal in the replication cycle of IAV.In this study,we found that BinCARD1,an isoform of Bcl10-interacting protein with CARD(BinCARD),was leveraged by IAV for efficient viral replication.BinCARD1 promoted the nuclear import of the vRNP complex and newly synthesized NP and thus enhanced vRNP complex activity.Moreover,we found that BinCARD1 interacted with NP to promote NP binding to importinα7,an adaptor in the host nuclear import pathway.However,we also found that BinCARD1 promoted RIG-I-mediated innate immune signaling by mediating Lys63-linked polyubiquitination of TRAF3,and that TBK1 appeared to degrade BinCARD1.We showed that BinCARD1 was polyubiquitinated at residue K103 through a Lys63 linkage,which was recognized by the TBK1-p62 axis for autophagic degradation.Overall,our data demonstrate that IAV leverages BinCARD1 as an important host factor that promotes viral replication,and two mechanisms in the host defense system are triggered—innate immune signaling and autophagic degradation—to mitigate the promoting effect of BinCARD1 on the life cycle of IAV.
基金supported by the National Natural Science Foundation of China(32192453,32172847)the National Key Research and Development Program of China(2021YFD1800204)+1 种基金the Laboratory of Lingnan Modern Agriculture Project(NT2021007)the earmarked fund for CARS-41。
文摘Influenza A virus(IAV) commandeers numerous host cellular factors for successful replication. However, very few host factors have been revealed to be involved in the fusion of viral envelope and late endosomal membranes. In this study, we identified cation-dependent mannose-6-phosphate receptor(M6PR) as a crucial host factor for the replication of IAV. We found that siRNA knockdown of M6PR expression significantly reduced the growth titers of different subtypes of IAV, and that the inhibitory effect of M6PR siRNA treatment on IAV growth was overcome by the complement of exogenously expressed M6PR. When A549 cells were treated with siRNA targeting M6PR,the nuclear accumulation of viral nucleoprotein(NP) was dramatically inhibited at early timepoints post-infection, indicating that M6PR engages in the early stage of the IAV replication cycle. By investigating the role of M6PR in the individual entry and post-entry steps of IAV replication, we found that the downregulation of M6PR expression had no effect on attachment, internalization, early endosome trafficking,or late endosome acidification. However, we found that M6PR expression was critical for the fusion of viral envelope and late endosomal membranes. Of note, M6PR interacted with the hemagglutinin(HA) protein of IAV, and further studies showed that the lumenal domain of M6PR and the ectodomain of HA2 mediated the interaction and directly promoted the fusion of the viral and late endosomal membranes,thereby facilitating IAV replication. Together, our findings highlight the importance of the M6PR–HA interaction in the fusion of viral and late endosomal membranes during IAV replication.
基金supported by the grants from National Science Foundation of China(U20A20369)“Pearl River Talent Plan”Innovation and Entrepreneurship Team Project of Guangdong Province(2019ZT08Y464,China)+2 种基金Guangdong Basic and Applied Basic Research Foundation(2022B1515120085,China)Shenzhen Science and Technology Program(KQTD20190929173853397,China)Henan Provincial Key R&D and Promotion Special(Scientific Problem Tackling)(222102310344,China)。
文摘Aside from antibodies,peptides show great potential as immune checkpoint inhibitors(ICIs)due to several advantages,such as better tumor penetration and lower cost.Lymphocyte-activation gene 3(LAG-3)is an immune checkpoint which can induce T cell dysfunction through interaction with its soluble ligand fibrinogen like protein-1(FGL1).Here,we found that LAG-3 expression was higher than programmed cell death protein 1(PD-1)in multiple human cancers by TCGA databases,and successfully identified a LAG-3 binding peptide LFP-6 by phage display bio-panning,which specifically blocks the interaction of LAG-3/FGL1 but not LAG-3/MHC-II.Subsequently,D-amino acids were introduced to substitute the N-and C-terminus of LFP-6 to obtain the proteolysis-resistant peptide LFP-D1,which restores T cell function in vitro and inhibits tumor growth in vivo.Further,a bispecific peptide LFOP targeting both PD-1/PD-L1 and LAG-3/FGL1 was designed by conjugating LFP-D1 with PD-1/PD-L1blocking peptide OPBP-1(8-12),which activates T cell with enhanced proliferation and IFN-γ production.More importantly,LFOP combined with radiotherapy significantly improve the T cell infiltration in tumor and elevate systemic antitumor immune response.In conclusion,we developed a novel peptide blocking LAG-3/FGL1 which can restore T cell function,and the bispecific peptide synergizes with radiotherapy to further enhance the antitumor immune response.
