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Duo H, Chhabra R, Muthusamy V, Dutta S, Katral A, Sarma GR, Chand G, Mishra SJ, Zunjare RU, Hossain F. Allelic Diversity and Development of Breeder-Friendly Marker Specific to floury2 Gene Regulating the Accumulation of α-Zeins and Essential Amino Acids in Maize Kernel. Biochem Genet 2024:10.1007/s10528-024-10935-x. [PMID: 39369369 DOI: 10.1007/s10528-024-10935-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 09/23/2024] [Indexed: 10/07/2024]
Abstract
Maize zeins lack essential amino acids, such as methionine, lysine, and tryptophan. The floury2 (fl2) mutation reduces zein synthesis and increases methionine and lysine content in kernels. In this study, fl2 gene (1612 bp) was sequenced in eight wild-type and two mutant inbreds and detected 218 SNPs and 18 InDels. Transversion of C to T at 343 bp position caused the substitution of alanine by valine in the fl2 mutant. A PCR-based marker (FL-SNP-CT) was developed, which distinguished the favorable mutant fl2 allele (T) from the wild-type (C) Fl2 allele. Gene-based diversity analysis using seven gene-based InDel markers grouped 48 inbred lines into three major clusters, with an average genetic dissimilarity coefficient of 0.534. The average major allele frequency, gene diversity, heterozygosity, and polymorphism information content of the InDel markers were 0.701, 0.392, 0.039, and 0.318, respectively. Haplotype analysis revealed 29 haplotypes of fl2 gene among these 48 inbreds. Amino acid substitution (Ala-Val) at the signal peptide cleavage site produced unprocessed 24-kDa mutant protein instead of 22-kDa zein found in normal genotype. Eight paralogues of fl2 detected in the study showed variation in exon lengths (616-1170 bp) and translation lengths (135-267 amino acids). Orthologue analysis among 15 accessions of Sorghum bicolor and two accessions of Saccharum spontaneum revealed a single exon in fl2 gene, ranging from 267 to 810 bp. The study elucidated the molecular basis of fl2 mutation and reported a breeder-friendly marker for molecular breeding programs. This is the first study to characterize fl2 gene in a set of subtropically adapted inbreds.
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Affiliation(s)
- Hriipulou Duo
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rashmi Chhabra
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Suman Dutta
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Gulab Chand
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Subhra J Mishra
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Firoz Hossain
- ICAR-Indian Agricultural Research Institute, New Delhi, India.
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2
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Mou SJ, Angon PB. Genome-wide characterization and expression profiling of FARL (FHY3/FAR1) family genes in Zea mays. J Genet Eng Biotechnol 2024; 22:100401. [PMID: 39179323 PMCID: PMC11342881 DOI: 10.1016/j.jgeb.2024.100401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 08/26/2024]
Abstract
A significant role of the plant is played by the transcription factor FARL, which is light signal transduction as well as plant growth and development. Despite being transposases, FARL has developed a variety of dominant biological actions in evolution and speciation. On the other hand, little is known about the Zea mays FARL protein family. This study identifies and characterizes fifteen ZmFARL genes genome-wide, and RNA sequencing data was used to profile their expression. 105 FARL proteins from five plant species were classified into five groups based on sequence alignment and phylogeny. The ZmFARL genes' exon-intron and motif distribution were conserved based on their evolutionary group. The fifteen ZmFARL genes were distributed over seven of the ten Z. mays chromosomes, although no duplication was discovered. Cis-element analysis reveals that ZmFARL genes play a variety of activities, including tissue-specific, stress- and hormone-responsive expressions. Furthermore, the results of the RNA sequencing used to profile expression showed that the genes ZmFARL2 and ZmFARL5 were much more expressed than other genes in various tissues, particularly in leaf characteristics. The identification of likely genes involved in cellular activity in Z. mays and related species will be aided by the characterization of the FARL genes.
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Affiliation(s)
- Sharah Jabeen Mou
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Prodipto Bishnu Angon
- Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
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3
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Pham D, Sivalingam V, Tang HM, Montgomery JM, Chen SCA, Halliday CL. Molecular Diagnostics for Invasive Fungal Diseases: Current and Future Approaches. J Fungi (Basel) 2024; 10:447. [PMID: 39057332 PMCID: PMC11278267 DOI: 10.3390/jof10070447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Invasive fungal diseases (IFDs) comprise a growing healthcare burden, especially given the expanding population of immunocompromised hosts. Early diagnosis of IFDs is required to optimise therapy with antifungals, especially in the setting of rising rates of antifungal resistance. Molecular techniques including nucleic acid amplification tests and whole genome sequencing have potential to offer utility in overcoming limitations with traditional phenotypic testing. However, standardisation of methodology and interpretations of these assays is an ongoing undertaking. The utility of targeted Aspergillus detection has been well-defined, with progress in investigations into the role of targeted assays for Candida, Pneumocystis, Cryptococcus, the Mucorales and endemic mycoses. Likewise, whilst broad-range polymerase chain reaction assays have been in use for some time, pathology stewardship and optimising diagnostic yield is a continuing exercise. As costs decrease, there is also now increased access and experience with whole genome sequencing, including metagenomic sequencing, which offers unparalleled resolution especially in the investigations of potential outbreaks. However, their role in routine diagnostic use remains uncommon and standardisation of techniques and workflow are required for wider implementation.
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Affiliation(s)
- David Pham
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Varsha Sivalingam
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Helen M. Tang
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - James M. Montgomery
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
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Xuan G, Xun L, Xia Y. MarR family proteins sense sulfane sulfur in bacteria. MLIFE 2024; 3:231-239. [PMID: 38948149 PMCID: PMC11211675 DOI: 10.1002/mlf2.12109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/12/2023] [Accepted: 12/24/2023] [Indexed: 07/02/2024]
Abstract
Members of the multiple antibiotic resistance regulator (MarR) protein family are ubiquitous in bacteria and play critical roles in regulating cellular metabolism and antibiotic resistance. MarR family proteins function as repressors, and their interactions with modulators induce the expression of controlled genes. The previously characterized modulators are insufficient to explain the activities of certain MarR family proteins. However, recently, several MarR family proteins have been reported to sense sulfane sulfur, including zero-valent sulfur, persulfide (R-SSH), and polysulfide (R-SnH, n ≥ 2). Sulfane sulfur is a common cellular component in bacteria whose levels vary during bacterial growth. The changing levels of sulfane sulfur affect the expression of many MarR-controlled genes. Sulfane sulfur reacts with the cysteine thiols of MarR family proteins, causing the formation of protein thiol persulfide, disulfide bonds, and other modifications. Several MarR family proteins that respond to reactive oxygen species (ROS) also sense sulfane sulfur, as both sulfane sulfur and ROS induce the formation of disulfide bonds. This review focused on MarR family proteins that sense sulfane sulfur. However, the sensing mechanisms reviewed here may also apply to other proteins that detect sulfane sulfur, which is emerging as a modulator of gene regulation.
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Affiliation(s)
- Guanhua Xuan
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
- State Key Laboratory of Marine Food Processing & Safety ControlOcean University of ChinaQingdaoChina
| | - Luying Xun
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
- School of Molecular BiosciencesWashington State UniversityPullmanWashingtonUSA
| | - Yongzhen Xia
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
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Itoh H, Yamashita H, Wada KC, Yonemaru JI. Real-time emulation of future global warming reveals realistic impacts on the phenological response and quality deterioration in rice. Proc Natl Acad Sci U S A 2024; 121:e2316497121. [PMID: 38739807 PMCID: PMC11126993 DOI: 10.1073/pnas.2316497121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 04/01/2024] [Indexed: 05/16/2024] Open
Abstract
Decreased production of crops due to climate change has been predicted scientifically. While climate-resilient crops are necessary to ensure food security and support sustainable agriculture, predicting crop growth under future global warming is challenging. Therefore, we aimed to assess the impact of realistic global warming conditions on rice cultivation. We developed a crop evaluation platform, the agro-environment (AE) emulator, which generates diverse environments by implementing the complexity of natural environmental fluctuations in customized, fully artificial lighting growth chambers. We confirmed that the environmental responsiveness of rice obtained in the fluctuation of artificial environments is similar to those exhibited in natural environments by validating our AE emulator using publicly available meteorological data from multiple years at the same location and multiple locations in the same year. Based on the representative concentration pathway, real-time emulation of severe global warming unveiled dramatic advances in the rice life cycle, accompanied by a 35% decrease in grain yield and an 85% increase in quality deterioration, which is higher than the recently reported projections. The transcriptome dynamism showed that increasing temperature and CO2 concentrations synergistically changed the expression of various genes and strengthened the induction of flowering, heat stress adaptation, and CO2 response genes. The predicted severe global warming greatly alters rice environmental adaptability and negatively impacts rice production. Our findings offer innovative applications of artificial environments and insights for enhancing varietal potential and cultivation methods in the future.
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Affiliation(s)
- Hironori Itoh
- Breeding Big Data Management and Utilization Group, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8518, Japan
| | - Hiroto Yamashita
- Breeding Big Data Management and Utilization Group, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8518, Japan
| | - Kaede C. Wada
- Breeding Big Data Management and Utilization Group, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8518, Japan
- Incubation Laboratory, Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-0856, Japan
| | - Jun-ichi Yonemaru
- Incubation Laboratory, Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-0856, Japan
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Raj-Kumar PK, Lin X, Liu T, Sturtz LA, Gritsenko MA, Petyuk VA, Sagendorf TJ, Deyarmin B, Liu J, Praveen-Kumar A, Wang G, McDermott JE, Shukla AK, Moore RJ, Monroe ME, Webb-Robertson BJM, Hooke JA, Fantacone-Campbell L, Mostoller B, Kvecher L, Kane J, Melley J, Somiari S, Soon-Shiong P, Smith RD, Mural RJ, Rodland KD, Shriver CD, Kovatich AJ, Hu H. Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection. Breast Cancer Res 2024; 26:76. [PMID: 38745208 PMCID: PMC11094977 DOI: 10.1186/s13058-024-01835-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/05/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. METHODS We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers. RESULTS We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations in TP53, PLXNB3, Zinc finger genes, and fewer mutations in SDC2, CDH1, PIK3CA, SVIL, and PTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA-protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, including KIAA1522, DCK, FOXO3, MYO9B, ARID1A, EPRS, ZC3HAV1, and RBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors. CONCLUSIONS This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.
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Affiliation(s)
- Praveen-Kumar Raj-Kumar
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Xiaoying Lin
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Tao Liu
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lori A Sturtz
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | | | | | - Brenda Deyarmin
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | | | - Guisong Wang
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | | | - Anil K Shukla
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | - Jeffrey A Hooke
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Leigh Fantacone-Campbell
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Brad Mostoller
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Leonid Kvecher
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jennifer Kane
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Jennifer Melley
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Stella Somiari
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | | | | | - Richard J Mural
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | | | - Craig D Shriver
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- Department of Surgery, Walter Reed National Military Medical Center, Bethesda, MD, USA.
| | - Albert J Kovatich
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA.
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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Duo H, Chhabra R, Muthusamy V, Zunjare RU, Hossain F. Assessing sequence variation, haplotype analysis and molecular characterisation of aspartate kinase2 (ask2) gene regulating methionine biosynthesis in diverse maize inbreds. Mol Genet Genomics 2024; 299:7. [PMID: 38349549 DOI: 10.1007/s00438-024-02096-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 11/02/2023] [Indexed: 02/15/2024]
Abstract
Traditional maize grain is deficient in methionine, an essential amino acid required for proper growth and development in humans and poultry birds. Thus, development of high methionine maize (HMM) assumes great significance in alleviating malnutrition through sustainable and cost-effective approach. Of various genetic loci, aspartate kinase2 (ask2) gene plays a pivotal role in regulating methionine accumulation in maize. Here, we sequenced the entire ask2 gene of 5394 bp with 13 exons in five wild and five mutant maize inbreds to understand variation at nucleotide level. Sequence analysis revealed that an SNP in exon-13 caused thymine to adenine transversion giving rise to a favourable mutant allele associated with leucine to glutamine substitution in mutant ASK2 protein. Gene-based diversity analysis with 11 InDel markers grouped 48 diverse inbreds into three major clusters with an average genetic dissimilarity of 0.570 (range, 0.0-0.9). The average major allele frequency, gene diversity and PIC are 0.693, 0.408 and 0.341, respectively. A total of 45 haplotypes of the ask2 gene were identified among the maize inbreds. Evolutionary relationship analysis performed among 22 orthologues grouped them into five major clusters. The number of exons varied from 7 to 17, with length varying from 12 to 495 bp among orthologues. ASK2 protein with 565 amino acids was predicted to be in homo-dimeric state with lysine and tartaric acid as binding ligands. Amino acid kinase and ACT domains were found to be conserved in maize and orthologues. The study depicted the presence of enough genetic diversity in ask2 gene in maize, and development of HMM can be accelerated through introgression of favourable allele of ask2 into the parental lines of elite hybrids using molecular breeding.
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Affiliation(s)
- Hriipulou Duo
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rashmi Chhabra
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Firoz Hossain
- ICAR-Indian Agricultural Research Institute, New Delhi, India.
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8
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Smith AB, Ganguly DR, Moore M, Bowerman AF, Janapala Y, Shirokikh NE, Pogson BJ, Crisp PA. Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:818-839. [PMID: 37947266 PMCID: PMC10952913 DOI: 10.1111/tpj.16531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Transcript stability is an important determinant of its abundance and, consequently, translational output. Transcript destabilisation can be rapid and is well suited for modulating the cellular response. However, it is unclear the extent to which RNA stability is altered under changing environmental conditions in plants. We previously hypothesised that recovery-induced transcript destabilisation facilitated a phenomenon of rapid recovery gene downregulation (RRGD) in Arabidopsis thaliana (Arabidopsis) following light stress, based on mathematical calculations to account for ongoing transcription. Here, we test this hypothesis and investigate processes regulating transcript abundance and fate by quantifying changes in transcription, stability and translation before, during and after light stress. We adapt syringe infiltration to apply a transcriptional inhibitor to soil-grown plants in combination with stress treatments. Compared with measurements in juvenile plants and cell culture, we find reduced stability across a range of transcripts encoding proteins involved in RNA binding and processing. We also observe light-induced destabilisation of transcripts, followed by their stabilisation during recovery. We propose that this destabilisation facilitates RRGD, possibly in combination with transcriptional shut-off that was confirmed for HSP101, ROF1 and GOLS1. We also show that translation remains highly dynamic over the course of light stress and recovery, with a bias towards transcript-specific increases in ribosome association, independent of changes in total transcript abundance, after 30 min of light stress. Taken together, we provide evidence for the combinatorial regulation of transcription and stability that occurs to coordinate translation during light stress and recovery in Arabidopsis.
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Affiliation(s)
- Aaron B. Smith
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Diep R. Ganguly
- CSIRO Synthetic Biology Future Science PlatformCanberraAustralian Capital Territory2601Australia
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Marten Moore
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Andrew F. Bowerman
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Yoshika Janapala
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVictoria3800Australia
| | - Nikolay E. Shirokikh
- The John Curtin School of Medical Research, The Shine‐Dalgarno Centre for RNA InnovationThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Barry J. Pogson
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Peter A. Crisp
- School of Agriculture and Food SciencesThe University of QueenslandBrisbaneQueensland4072Australia
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Zakrzewska-Placzek M, Golisz-Mocydlarz A, Krzyszton M, Piotrowska J, Lichocka M, Kufel J. The nucleolar protein NOL12 is required for processing of large ribosomal subunit rRNA precursors in Arabidopsis. BMC PLANT BIOLOGY 2023; 23:538. [PMID: 37919659 PMCID: PMC10623804 DOI: 10.1186/s12870-023-04561-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/26/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND NOL12 5'-3' exoribonucleases, conserved among eukaryotes, play important roles in pre-rRNA processing, ribosome assembly and export. The most well-described yeast counterpart, Rrp17, is required for maturation of 5.8 and 25S rRNAs, whereas human hNOL12 is crucial for the separation of the large (LSU) and small (SSU) ribosome subunit rRNA precursors. RESULTS In this study we demonstrate that plant AtNOL12 is also involved in rRNA biogenesis, specifically in the processing of the LSU rRNA precursor, 27S pre-rRNA. Importantly, the absence of AtNOL12 alters the expression of many ribosomal protein and ribosome biogenesis genes. These changes could potentially exacerbate rRNA biogenesis defects, or, conversely, they might stem from the disturbed ribosome assembly caused by delayed pre-rRNA processing. Moreover, exposure of the nol12 mutant to stress factors, including heat and pathogen Pseudomonas syringae, enhances the observed molecular phenotypes, linking pre-rRNA processing to stress response pathways. The aberrant rRNA processing, dependent on AtNOL12, could impact ribosome function, as suggested by improved mutant resistance to ribosome-targeting antibiotics. CONCLUSION Despite extensive studies, the pre-rRNA processing pathway in plants remains insufficiently characterized. Our investigation reveals the involvement of AtNOL12 in the maturation of rRNA precursors, correlating this process to stress response in Arabidopsis. These findings contribute to a more comprehensive understanding of plant ribosome biogenesis.
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Affiliation(s)
- Monika Zakrzewska-Placzek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, Warsaw, 02-106, Poland.
| | - Anna Golisz-Mocydlarz
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, Warsaw, 02-106, Poland
| | - Michal Krzyszton
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw, 02-106, Poland
| | - Justyna Piotrowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw, 02-106, Poland
| | - Malgorzata Lichocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw, 02-106, Poland
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, Warsaw, 02-106, Poland.
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10
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Mourad AM, Hamdy RM, Esmail SM. Novel genomic regions on chromosome 5B controlling wheat powdery mildew seedling resistance under Egyptian conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1160657. [PMID: 37235018 PMCID: PMC10208068 DOI: 10.3389/fpls.2023.1160657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/27/2023] [Indexed: 05/28/2023]
Abstract
Wheat powdery mildew (PM) causes significant yield losses worldwide. None of the Egyptian wheat cultivars was detected to be highly resistant to such a severe disease. Therefore, a diverse spring wheat panel was evaluated for PM seedling resistance using different Bgt conidiospores collected from Egyptian fields in two growing seasons. The evaluation was done in two separate experiments. Highly significant differences were found between the two experiments suggesting the presence of different isolates populations. Highly significant differences were found among the tested genotypes confirming the ability to improve PM resistance using the recent panel. Genome-wide association study (GWAS) was done for each experiment separately and a total of 71 significant markers located within 36 gene models were identified. The majority of these markers are located on chromosome 5B. Haplotype block analysis identified seven blocks containing the significant markers on chromosome 5B. Five gene models were identified on the short arm of the chromosome. Gene enrichment analysis identified five and seven pathways based on the biological process and molecular functions respectively for the detected gene models. All these pathways are associated with disease resistance in wheat. The genomic regions on 5B seem to be novel regions that are associated with PM resistance under Egyptian conditions. Selection of superior genotypes was done and Grecian genotypes seem to be a good source for improving PM resistance under Egyptian conditions.
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Affiliation(s)
- Amira M.I. Mourad
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Rania M. Hamdy
- Food Science and Technology Department, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Samar M. Esmail
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
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11
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Marin de Mas I, Herand H, Carrasco J, Nielsen LK, Johansson PI. A Protocol for the Automatic Construction of Highly Curated Genome-Scale Models of Human Metabolism. Bioengineering (Basel) 2023; 10:bioengineering10050576. [PMID: 37237646 DOI: 10.3390/bioengineering10050576] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/24/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Genome-scale metabolic models (GEMs) have emerged as a tool to understand human metabolism from a holistic perspective with high relevance in the study of many diseases and in the metabolic engineering of human cell lines. GEM building relies on either automated processes that lack manual refinement and result in inaccurate models or manual curation, which is a time-consuming process that limits the continuous update of reliable GEMs. Here, we present a novel algorithm-aided protocol that overcomes these limitations and facilitates the continuous updating of highly curated GEMs. The algorithm enables the automatic curation and/or expansion of existing GEMs or generates a highly curated metabolic network based on current information retrieved from multiple databases in real time. This tool was applied to the latest reconstruction of human metabolism (Human1), generating a series of the human GEMs that improve and expand the reference model and generating the most extensive and comprehensive general reconstruction of human metabolism to date. The tool presented here goes beyond the current state of the art and paves the way for the automatic reconstruction of a highly curated, up-to-date GEM with high potential in computational biology as well as in multiple fields of biological science where metabolism is relevant.
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Affiliation(s)
- Igor Marin de Mas
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, 2800 Lyngby, Denmark
- CAG Center for Endotheliomics, Copenhagen University Hospital, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Helena Herand
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, 2800 Lyngby, Denmark
- CAG Center for Endotheliomics, Copenhagen University Hospital, 2100 Copenhagen, Denmark
| | - Jorge Carrasco
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, 2800 Lyngby, Denmark
| | - Lars K Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, 2800 Lyngby, Denmark
- CAG Center for Endotheliomics, Copenhagen University Hospital, 2100 Copenhagen, Denmark
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
| | - Pär I Johansson
- CAG Center for Endotheliomics, Copenhagen University Hospital, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, 1165 Copenhagen, Denmark
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12
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Chen L, Yang Y, Zhao Z, Lu S, Lu Q, Cui C, Parry MAJ, Hu YG. Genome-wide identification and comparative analyses of key genes involved in C 4 photosynthesis in five main gramineous crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1134170. [PMID: 36993845 PMCID: PMC10040670 DOI: 10.3389/fpls.2023.1134170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Compared to C3 species, C4 plants showed higher photosynthetic capacity as well as water and nitrogen use efficiency due to the presence of the C4 photosynthetic pathway. Previous studies have shown that all genes required for the C4 photosynthetic pathway exist in the genomes of C3 species and are expressed. In this study, the genes encoding six key C4 photosynthetic pathway enzymes (β-CA, PEPC, ME, MDH, RbcS, and PPDK) in the genomes of five important gramineous crops (C4: maize, foxtail millet, and sorghum; C3: rice and wheat) were systematically identified and compared. Based on sequence characteristics and evolutionary relationships, their C4 functional gene copies were distinguished from non-photosynthetic functional gene copies. Furthermore, multiple sequence alignment revealed important sites affecting the activities of PEPC and RbcS between the C3 and C4 species. Comparisons of expression characteristics confirmed that the expression patterns of non-photosynthetic gene copies were relatively conserved among species, while C4 gene copies in C4 species acquired new tissue expression patterns during evolution. Additionally, multiple sequence features that may affect C4 gene expression and subcellular localization were found in the coding and promoter regions. Our work emphasized the diversity of the evolution of different genes in the C4 photosynthetic pathway and confirmed that the specific high expression in the leaf and appropriate intracellular distribution were the keys to the evolution of C4 photosynthesis. The results of this study will help determine the evolutionary mechanism of the C4 photosynthetic pathway in Gramineae and provide references for the transformation of C4 photosynthetic pathways in wheat, rice, and other major C3 cereal crops.
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Affiliation(s)
- Liang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yang Yang
- College of Agriculture, Shannxi Agricultural University (Institute of Crop Sciences), Taiyuan, Shanxi, China
| | - Zhangchen Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Shan Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiumei Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Chunge Cui
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Martin A. J. Parry
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Yin-Gang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- Institute of Water Saving Agriculture in Arid Regions of China, Northwest A&F University, Yangling, Shaanxi, China
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13
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Motoshima T, Nagashima A, Ota C, Oka H, Hosono K, Braasch I, Nishihara H, Kato A. Na +/Cl - cotransporter 2 is not fish-specific and is widely found in amphibians, non-avian reptiles, and select mammals. Physiol Genomics 2023; 55:113-131. [PMID: 36645671 PMCID: PMC9988527 DOI: 10.1152/physiolgenomics.00143.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/28/2022] [Accepted: 01/12/2023] [Indexed: 01/17/2023] Open
Abstract
Solute carrier 12 (Slc12) is a family of electroneutral cation-coupled chloride (Cl-) cotransporters. Na+/K+/2Cl- (Nkcc) and Na+/Cl- cotransporters (Ncc) belong to the Nkcc/Ncc subfamily. Human and mouse possess one gene for the Na+/Cl- cotransporter (ncc gene: slc12a3), whereas teleost fishes possess multiple ncc genes, slc12a3 (ncc1) and slc12a10 (ncc2), in addition to their species-specific paralogs. Amphibians and squamates have two ncc genes: slc12a3 (ncc1) and ncc3. However, the evolutionary relationship between slc12a10 and ncc3 remains unresolved, and the presence of slc12a10 (ncc2) in mammals has not been clarified. Synteny and phylogenetic analyses of vertebrate genome databases showed that ncc3 is the ortholog of slc12a10, and slc12a10 is present in most ray-finned fishes, coelacanths, amphibians, reptiles, and a few mammals (e.g., platypus and horse) but pseudogenized or deleted in birds, most mammals, and some ray-finned fishes (pufferfishes). This shows that slc12a10 is widely present among bony vertebrates and pseudogenized or deleted independently in multiple lineages. Notably, as compared with some fish that show varied slc12a10 tissue expression profile, spotted gar, African clawed frog, red-eared slider turtle, and horse express slc12a10 in the ovaries or premature gonads. In horse tissues, an unexpectedly large number of splicing variants for Slc12a10 have been cloned, many of which encode truncated forms of Slc12a10, suggesting that the functional constraints of horse slc12a10 are weakened, which may be in the process of becoming a pseudogene. Our results elaborate on the evolution of Nkcc/Ncc subfamily of Slc12 in vertebrates.NEW & NOTEWORTHY slc12a10 is not a fish-specific gene and is present in a few mammals (e.g., platypus and horse), non-avian reptiles, amphibians, but was pseudogenized or deleted in most mammals (e.g., human, mouse, cat, cow, and rhinoceros), birds, and some ray-finned fishes (pufferfishes).
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Affiliation(s)
- Toya Motoshima
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ayumi Nagashima
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Chihiro Ota
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Haruka Oka
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kohei Hosono
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ingo Braasch
- Department of Integrative Biology, College of Natural Science, Michigan State University, East Lansing, Michigan, United States
| | - Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Akira Kato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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14
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Kui L, Majeed A, Wang X, Yang Z, Chen J, He L, Di Y, Li X, Qian Z, Jiao Y, Wang G, Liu L, Xu R, Gu S, Yang Q, Chen S, Lou H, Meng Y, Xie L, Xu F, Shen Q, Singh A, Gruber K, Pan Y, Hao T, Dong Y, Li F. A chromosome-level genome assembly for Erianthus fulvus provides insights into its biofuel potential and facilitates breeding for improvement of sugarcane. PLANT COMMUNICATIONS 2023:100562. [PMID: 36814384 PMCID: PMC10363513 DOI: 10.1016/j.xplc.2023.100562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/21/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Erianthus produces substantial biomass, exhibits a good Brix value, and shows wide environmental adaptability, making it a potential biofuel plant. In contrast to closely related sorghum and sugarcane, Erianthus can grow in degraded soils, thus releasing pressure on agricultural lands used for biofuel production. However, the lack of genomic resources for Erianthus hinders its genetic improvement, thus limiting its potential for biofuel production. In the present study, we generated a chromosome-scale reference genome for Erianthus fulvus Nees. The genome size estimated by flow cytometry was 937 Mb, and the assembled genome size was 902 Mb, covering 96.26% of the estimated genome size. A total of 35 065 protein-coding genes were predicted, and 67.89% of the genome was found to be repetitive. A recent whole-genome duplication occurred approximately 74.10 million years ago in the E. fulvus genome. Phylogenetic analysis showed that E. fulvus is evolutionarily closer to S. spontaneum and diverged after S. bicolor. Three of the 10 chromosomes of E. fulvus formed through rearrangements of ancestral chromosomes. Phylogenetic reconstruction of the Saccharum complex revealed a polyphyletic origin of the complex and a sister relationship of E. fulvus with Saccharum sp., excluding S. arundinaceum. On the basis of the four amino acid residues that provide substrate specificity, the E. fulvus SWEET proteins were classified as mono- and disaccharide sugar transporters. Ortho-QTL genes identified for 10 biofuel-related traits may aid in the rapid screening of E. fulvus populations to enhance breeding programs for improved biofuel production. The results of this study provide valuable insights for breeding programs aimed at improving biofuel production in E. fulvus and enhancing sugarcane introgression programs.
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Affiliation(s)
- Ling Kui
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen 518067, China
| | - Aasim Majeed
- Plant Molecular Genetics Laboratory, School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Xianhong Wang
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China; The Key Laboratory of Crop Production and Smart Agriculture of Yunnan Province, Kunming, Yunnan 650201, China
| | - Zijiang Yang
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Jian Chen
- International Genome Center, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Lilian He
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Yining Di
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Xuzhen Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, Yunnan 650201, China
| | - Zhenfeng Qian
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Yinming Jiao
- Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen 518067, China
| | - Guoyun Wang
- Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen 518067, China
| | - Lufeng Liu
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; The Key Laboratory of Crop Production and Smart Agriculture of Yunnan Province, Kunming, Yunnan 650201, China
| | - Rong Xu
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Shujie Gu
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Qinghui Yang
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Shuying Chen
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Hongbo Lou
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Yu Meng
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Linyan Xie
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Fu Xu
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Qingqing Shen
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Amit Singh
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Yunbing Pan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, Yunnan 650201, China
| | - Tingting Hao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, Yunnan 650201, China
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, Yunnan 650201, China.
| | - Fusheng Li
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China; The Key Laboratory of Crop Production and Smart Agriculture of Yunnan Province, Kunming, Yunnan 650201, China.
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15
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A receptor-like kinase controls the amplitude of secondary cell wall synthesis in rice. Curr Biol 2023; 33:498-506.e6. [PMID: 36638797 DOI: 10.1016/j.cub.2022.12.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/06/2022] [Accepted: 12/13/2022] [Indexed: 01/14/2023]
Abstract
Cell wall expansion is a key element in determining plant morphology and growth, and cell wall integrity changes are relayed to the cell to fine-tune growth responses. Here, we show that variations in the ectodomain of a cell wall-associated receptor-like kinase, WAK10, in temperate Oryza japonica accessions differentially amplify fluctuations in cell wall integrity to control rice stem height. Mutation in the WAK10 gene exhibited increased cell wall thickening in stem sclerenchyma and reduced cell expansion in the stem. Two WAK10 ectodomain variants bound pectic oligosaccharides with different affinities. The pectic oligosaccharide binding regulated WAK10 phosphorylation activity, the amplitude of secondary wall deposition, and ultimately, stem height. Rice population analyses revealed active enrichment of the short-stem WAK10 ectodomain alleles in japonica subspecies during domestication. Our study outlines not only a mechanism for how variations in ligand affinities of a receptor kinase control cell wall biosynthesis and plant growth, but it also provides breeding targets for new semi-dwarf rice cultivars.
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16
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Morrow JD, Castaldi PJ, Chase RP, Yun JH, Kinney GL, Silverman EK, Hersh CP. Hepatitis C and HIV detection by blood RNA-sequencing in cohort of smokers. Sci Rep 2023; 13:1357. [PMID: 36693932 PMCID: PMC9873751 DOI: 10.1038/s41598-023-28156-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023] Open
Abstract
Detection of viruses by RNA and DNA sequencing has improved the understanding of the human virome. We sought to identify blood viral signatures through secondary use of RNA-sequencing (RNA-seq) data in a large study cohort. The ability to reveal undiagnosed infections with public health implications among study subjects with available sequencing data could enable epidemiologic surveys and may lead to diagnosis and therapeutic interventions, leveraging existing research data in a clinical context. We detected viral RNA in peripheral blood RNA-seq data from a COPD-enriched population of current and former smokers. Correlation between viral detection and both reported infections and relevant disease outcomes was evaluated. We identified Hepatitis C virus RNA in 228 subjects and HIV RNA in 30 subjects. Overall, we observed 31 viral species, including Epstein-Barr virus and Cytomegalovirus. We observed an enrichment of Hepatitis C and HIV infections among subjects reporting liver disease and HIV infections, respectively. Higher interferon expression scores were observed in the subjects with Hepatitis C and HIV infections. Through secondary use of RNA-seq from a cohort of current and former smokers, we detected peripheral blood viral signatures. We identified HIV and Hepatitis C virus (HCV), highlighting potential public health implications for the approach described this study. We observed correlations with reported infections, chronic infection outcomes and the host transcriptomic response, providing evidence to support the validity of the approach.
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Affiliation(s)
- Jarrett D Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Robert P Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Jeong H Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Gregory L Kinney
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
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17
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Fullam A, Letunic I, Schmidt TSB, Ducarmon QR, Karcher N, Khedkar S, Kuhn M, Larralde M, Maistrenko O, Malfertheiner L, Milanese A, Rodrigues J, Sanchis-López C, Schudoma C, Szklarczyk D, Sunagawa S, Zeller G, Huerta-Cepas J, von Mering C, Bork P, Mende DR. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic Acids Res 2023; 51:D760-D766. [PMID: 36408900 PMCID: PMC9825469 DOI: 10.1093/nar/gkac1078] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/15/2022] [Accepted: 11/07/2022] [Indexed: 11/22/2022] Open
Abstract
The interpretation of genomic, transcriptomic and other microbial 'omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http://progenomes.embl.de/.
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Affiliation(s)
- Anthony Fullam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Ivica Letunic
- Biobyte solutions GmbH, Bothestr. 142, 69117 Heidelberg, Germany
| | - Thomas S B Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Quinten R Ducarmon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Nicolai Karcher
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Supriya Khedkar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Michael Kuhn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Martin Larralde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Oleksandr M Maistrenko
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology & Biogeochemistry, 1797 SZ, ’t Horntje (Texel), Netherlands
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alessio Milanese
- Institute of Microbiology, Department of Biology and Swiss Institute of Bioinformatics, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | | | - Claudia Sanchis-López
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Christian Schudoma
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Damian Szklarczyk
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Shinichi Sunagawa
- Institute of Microbiology, Department of Biology and Swiss Institute of Bioinformatics, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, 03722 Seoul, South Korea
| | - Daniel R Mende
- Department of Medical Microbiology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
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18
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Fernandez-Pozo N. PEATmoss: A Gene Expression Atlas for Bryophytes. Methods Mol Biol 2023; 2703:91-107. [PMID: 37646940 DOI: 10.1007/978-1-0716-3389-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
PEATmoss is an interactive gene expression atlas for bryophytes, which originally unified Physcomitrium patens RNA-seq and microarray expression data from multiple gene annotation versions. This atlas includes more than 100 experiments of P. patens, is expanding to host Anthoceros agrestis and Marchantia polymorpha, and aims to host data from more species in the future. PEATmoss has multiple visualization methods and tools for data downloading and is connected to the Physcomitrium patens Gene Model Lookup DB (PpGML DB), which links P. patens genes to annotations and resources from several databases and contains tools for gene version lookup and sequence and annotation extraction. Among the new features available in PEATmoss are dataset privacy control, multispecies menu, interactive color scale, co-expression network visualization, and replicate data downloading.
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Affiliation(s)
- Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany.
- Institute for Mediterranean and Subtropical Horticulture (IHSM-CSIC-UMA), Algarrobo-Costa, Málaga, Spain.
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19
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Papa Y, Wellenreuther M, Morrison MA, Ritchie PA. Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus). G3 (BETHESDA, MD.) 2022; 13:6883520. [PMID: 36477875 PMCID: PMC9911067 DOI: 10.1093/g3journal/jkac315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 12/14/2022]
Abstract
Although being some of the most valuable and heavily exploited wild organisms, few fisheries species have been studied at the whole-genome level. This is especially the case in New Zealand, where genomics resources are urgently needed to assist fisheries management. Here, we generated 55 Gb of short Illumina reads (92× coverage) and 73 Gb of long Nanopore reads (122×) to produce the first genome assembly of the marine teleost tarakihi [Nemadactylus macropterus (Forster, 1801)], a highly valuable fisheries species in New Zealand. An additional 300 Mb of Iso-Seq reads were obtained to assist in gene annotation. The final genome assembly was 568 Mb long with an N50 of 3.37 Mb. The genome completeness was high, with 97.8% of complete Actinopterygii Benchmarking Universal Single-Copy Orthologs. Heterozygosity values estimated through k-mer counting (1.00%) and bi-allelic SNPs (0.64%) were high compared with the same values reported for other fishes. Iso-Seq analysis recovered 91,313 unique transcripts from 15,515 genes (mean ratio of 5.89 transcripts per gene), and the most common alternative splicing event was intron retention. This highly contiguous genome assembly and the isoform-resolved transcriptome will provide a useful resource to assist the study of population genomics and comparative eco-evolutionary studies in teleosts and related organisms.
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Affiliation(s)
- Yvan Papa
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Maren Wellenreuther
- Seafood Production Group, The New Zealand Institute for Plant and Food Research Limited, Nelson 7010, New Zealand,School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Mark A Morrison
- National Institute of Water and Atmospheric Research, Auckland 1010, New Zealand
| | - Peter A Ritchie
- Corresponding author: Te Toki A Rata, Gate 7, Kelburn Parade, Wellington 6012, New Zealand.
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20
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Zhang X, Smith DR. An overview of online resources for intra-species detection of gene duplications. Front Genet 2022; 13:1012788. [PMID: 36313461 PMCID: PMC9606816 DOI: 10.3389/fgene.2022.1012788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Gene duplication plays an important role in evolutionary mechanism, which can act as a new source of genetic material in genome evolution. However, detecting duplicate genes from genomic data can be challenging. Various bioinformatics resources have been developed to identify duplicate genes from single and/or multiple species. Here, we summarize the metrics used to measure sequence identity among gene duplicates within species, compare several computational approaches that have been used to predict gene duplicates, and review recent advancements of a Basic Local Alignment Search Tool (BLAST)-based web tool and database, allowing future researchers to easily identify intra-species gene duplications. This article is a quick reference guide for research tools used for detecting gene duplicates.
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Affiliation(s)
- Xi Zhang
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
| | - David Roy Smith
- Department of Biology, Western University, London, ON, Canada
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21
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Wu AC, Vivori C, Patel H, Sideri T, Moretto F, van Werven FJ. RSC and GRFs confer promoter directionality by restricting divergent noncoding transcription. Life Sci Alliance 2022; 5:e202201394. [PMID: 36114005 PMCID: PMC9481977 DOI: 10.26508/lsa.202201394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/24/2022] Open
Abstract
The directionality of gene promoters-the ratio of protein-coding over divergent noncoding transcription-is highly variable. How promoter directionality is controlled remains poorly understood. Here, we show that the chromatin remodelling complex RSC and general regulatory factors (GRFs) dictate promoter directionality by attenuating divergent transcription relative to protein-coding transcription. At gene promoters that are highly directional, depletion of RSC leads to a relative increase in divergent noncoding transcription and thus to a decrease in promoter directionality. We find that RSC has a modest effect on nucleosome positioning upstream in promoters at the sites of divergent transcription. These promoters are also enriched for the binding of GRFs such as Reb1 and Abf1. Ectopic targeting of divergent transcription initiation sites with GRFs or the dCas9 DNA-binding protein suppresses divergent transcription. Our data suggest that RSC and GRFs play a pervasive role in limiting divergent transcription relative to coding direction transcription. We propose that any DNA-binding factor, when stably associated with cryptic transcription start sites, forms a barrier which represses divergent transcription, thereby promoting promoter directionality.
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Affiliation(s)
- Andrew Ck Wu
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Claudia Vivori
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Theodora Sideri
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Fabien Moretto
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Greece
| | - Folkert J van Werven
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
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22
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Belinky F, Bykova A, Yurchenko V, Rogozin IB. No evidence for widespread positive selection on double substitutions within codons in primates and yeasts. Front Genet 2022; 13:991249. [PMID: 36159983 PMCID: PMC9500374 DOI: 10.3389/fgene.2022.991249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Nucleotide substitutions in protein-coding genes can be divided into synonymous (S) and non-synonymous (N) ones that alter amino acids (including nonsense mutations causing stop codons). The S substitutions are expected to have little effect on function. The N substitutions almost always are affected by strong purifying selection that eliminates them from evolving populations. However, additional mutations of nearby bases can modulate the deleterious effect of single N substitutions and, thus, could be subjected to the positive selection. This effect has been demonstrated for mutations in the serine codons, stop codons and double N substitutions in prokaryotes. In all abovementioned cases, a novel technique was applied that allows elucidating the effects of selection on double substitutions considering mutational biases. Here, we applied the same technique to study double N substitutions in eukaryotic lineages of primates and yeast. We identified markedly fewer cases of purifying selection relative to prokaryotes and no evidence of codon double substitutions under positive selection. This is consistent with previous studies of serine codons in primates and yeast. In general, the obtained results strongly suggest that there are major differences between studied pro- and eukaryotes; double substitutions in primates and yeasts largely reflect mutational biases and are not hallmarks of selection. This is especially important in the context of detection of positive selection in codons because it has been suggested that multiple mutations in codons cause false inferences of lineage-specific site positive selection. It is likely that this concern is applicable to previously studied prokaryotes but not to primates and yeasts where markedly fewer double substitutions are affected by positive selection.
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Affiliation(s)
- Frida Belinky
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Anastassia Bykova
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- *Correspondence: Vyacheslav Yurchenko, ; Igor B. Rogozin,
| | - Igor B. Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Vyacheslav Yurchenko, ; Igor B. Rogozin,
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Zhu X, Wang B, Wei X, Du X. Characterization of the CqCAMTA gene family reveals the role of CqCAMTA03 in drought tolerance. BMC PLANT BIOLOGY 2022; 22:428. [PMID: 36071408 PMCID: PMC9450354 DOI: 10.1186/s12870-022-03817-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Calmodulin-binding transcription activators (CAMTAs) are relatively conserved calmodulin-binding transcription factors widely found in eukaryotes and play important roles in plant growth and stress response. CAMTA transcription factors have been identified in several plant species, but the family members and functions have not yet been identified and analyzed in quinoa. RESULTS In this study, we identified seven CAMTA genes across the whole quinoa genome and analyzed the expression patterns of CqCAMTAs in root and leaf tissues. Gene structure, protein domain, and phylogenetic analyses showed that the quinoa CAMTAs were structurally similar and clustered into the same three major groups as other plant CAMTAs. A large number of stress response-related cis-elements existed in the 2 kb promoter region upstream of the transcription start site of the CqCAMTA genes. qRT-PCR indicated that CqCAMTA genes were expressed differentially under PEG treatments in leaves, and responded to drought stress in leaves and roots. In particular, the CqCAMTA03 gene strongly responded to drought. The transient expression of CqCAMTA03-GFP fusion protein in the tobacco leaf showed that CqCAMTA03 was localized in the nucleus. In addition, transgenic Arabidopsis lines exhibited higher concentration levels of the antioxidant enzymes measured, including POD, SOD, and CAT, under drought conditions with very low levels of H2O2 and MDA. Moreover, relative water content and the degree of stomatal opening showed that the transgenic Arabidopsis lines were more tolerant of both stress factors as compared to their wild types. CONCLUSION In this study, the structures and functions of the CAMTA family in quinoa were systematically explored. Many CAMTAs may play vital roles in the regulation of organ development, growth, and responses to drought stress. The results of the present study serve as a basis for future functional studies on the quinoa CAMTA family.
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Affiliation(s)
- Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Baoqiang Wang
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiaohong Wei
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Xuefeng Du
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
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24
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Liu Z, Fan H, Ma Z. Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses. THE PLANT GENOME 2022; 15:e20226. [PMID: 35713030 DOI: 10.1002/tpg2.20226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/14/2021] [Indexed: 06/15/2023]
Abstract
Foxtail millet [Setaria italica (L.) P. Beauv.] does not show high yield and biomass compared with maize (Zea mays L.) although it is a C4 crop with the potential for high productivity. Because SWEET genes, which are important for sugar transport in plants, play critical roles in biomass production and seed filling in crops, genome-wide, transcriptomic, and proteomic comparison on SWEET gene family between these two species would provide some clues for unlocking this issue. In our study, 24 SWEET genes were identified in foxtail millet and maize. Sequence-based bioinformatics combined with gene expression analyses identified several candidate functional orthologs in these two species. A comparative analysis on expression characteristics of SWEET genes and proteins between maize and foxtail millet indicate that not only some critical major SWEET proteins show significant upregulation in maize compared with their orthologs in foxtail millet, but also there are more quantities of maize SWEET genes showing high expressions than that of foxtail millet genes, suggesting that compared with foxtail millet, maize possesses higher capacity of sugar transport, the crucial determinant for crop yield and biomass. These results provide a basis on revealing why foxtail millet exhibits low yield and biomass although it is a C4 crop with the potential for high productivity.
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Affiliation(s)
- Zheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural Univ., Baoding, Hebei, 071001, People's Republic of China
| | - Hui Fan
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural Univ., Baoding, Hebei, 071001, People's Republic of China
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural Univ., Baoding, Hebei, 071001, People's Republic of China
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Zhou X, Huang K, Teng C, Abdelgawad A, Batish M, Meyers BC, Walbot V. 24-nt phasiRNAs move from tapetal to meiotic cells in maize anthers. THE NEW PHYTOLOGIST 2022; 235:488-501. [PMID: 35451503 DOI: 10.1111/nph.18167] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
In maize, 24-nt phased, secondary small interfering RNAs (phasiRNAs) are abundant in meiotic stage anthers, but their distribution and functions are not precisely known. Using laser capture microdissection, we analyzed tapetal cells, meiocytes and other somatic cells at several stages of anther development to establish the timing of 24-PHAS precursor transcripts and the 24-nt phasiRNA products. By integrating RNA and small RNA profiling plus single-molecule and small RNA FISH (smFISH or sRNA-FISH) spatial detection, we demonstrate that the tapetum is the primary site of 24-PHAS precursor and Dcl5 transcripts and the resulting 24-nt phasiRNAs. Interestingly, 24-nt phasiRNAs accumulate in all cell types, with the highest levels in meiocytes, followed by tapetum. Our data support the conclusion that 24-nt phasiRNAs are mobile from tapetum to meiocytes and to other somatic cells. We discuss possible roles for 24-nt phasiRNAs in anther cell types.
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Affiliation(s)
- Xue Zhou
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Kun Huang
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19716, USA
- Dana-Farber Cancer Institute Molecular Imaging Core, 360 Longwood Ave, Boston, MA, 02215, USA
| | - Chong Teng
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Ahmed Abdelgawad
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
- Division of Plant Sciences, University of Missouri - Columbia, Columbia, MO, 65211, USA
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
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26
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Jin Y, Yu J, Jiang Y, Bu J, Zhu T, Gu X, Zhu X. Comprehensive analysis of the expression, prognostic significance, and function of FAM83 family members in breast cancer. World J Surg Oncol 2022; 20:172. [PMID: 35650627 PMCID: PMC9158143 DOI: 10.1186/s12957-022-02636-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The FAM83 family plays a key role in tumorigenesis and cancer progression. However, the role of the FAM83 family in the development of breast tumors is unclear to date. This report explores the expression, prognostic significance, and function of the FAM83 family members in breast cancer using public databases. METHODS UALCAN database was used to explore the expression of FAM83 family members in breast cancer. Furthermore, we validated the expression of FAM83 family members in twenty pairs of breast cancer and normal tissues by RT-PCR. Kaplan-Meier plotter database was used to explore the prognostic significance of FAM83 family members in breast cancer. GeneMANIA and DAVID databases were used for functional and pathway enrichment analysis of genes co-expressed with FAM83A, FAM83D, FAM83F, and FAM83G. MEXPRESS and UALCAN databases were used to analyze the level of DNA promoter methylation of FAM83A, FAM83D, FAM83F, and FAM83G in breast cancer. TIMER database was utilized to explore the relationships between immune cell infiltration and FAM83A, FAM83D, FAM83F, and FAM83G expression. RESULTS Among FAM83 family members, FAM83A, FAM83D, FAM83F, and FAM83G were higher expressed in breast cancer than in normal tissues. We also validated the significant high expression of FAM83A, FAM83D, FAM83F, and FAM83G mRNA in breast cancer than in normal samples. Their increased expression has an adverse prognostic effect on breast cancer patients. These genes co-expressed with FAM83A, FAM83D, FAM83F, and FAM83G might take part in cell proliferation, G2/M transition of the mitotic cell cycle, regulation of apoptosis process and other cancer-related biological processes. In addition, they were mainly enriched in the Hippo signaling pathway, Hedgehog signaling pathway, PI3K/AKT signaling pathway, and other cancer-related pathways. We also found that promoter DNA methylation might regulate the expression of FAM83A, FAM83D, FAM83F, and FAM83G mRNA in most CpG islands. At last, we found the expression of FAM83A, FAM83D, FAM83F, and FAM83G mRNA was significantly related to immune cell infiltration. CONCLUSIONS FAM83A, FAM83D, FAM83F, and FAM83G were highly expressed in breast cancer tissues and had an adverse effect on the survival outcomes of breast cancer patients. Also, they were involved in breast cancer-related signal pathways. Therefore, they might serve as potential therapeutic targets for breast cancer clinical treatment.
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Affiliation(s)
- Yi Jin
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning, 110042, People's Republic of China
| | - Jiahui Yu
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Yi Jiang
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Jiawen Bu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Tong Zhu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Xi Gu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China.
| | - Xudong Zhu
- Department of General Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning, 110042, People's Republic of China.
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Katral A, Muthusamy V, Zunjare RU, Chhabra R, Maman S, Yadava DK, Hossain F. Allelic Variation in Zmfatb Gene Defines Variability for Fatty Acids Composition Among Diverse Maize Genotypes. Front Nutr 2022; 9:845255. [PMID: 35600823 PMCID: PMC9120846 DOI: 10.3389/fnut.2022.845255] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Edible oil with lower saturated fatty acids is desired for perceived quality and health benefits to humans and livestock. fatb gene encoding acyl-ACP thioesterase is a key player in the conversion of palmitic acid to oleic acid, thereby modifying the ratio of saturated to unsaturated fatty acids in maize kernels. The present investigation characterised the full-length sequence of the Zmfatb gene (4.63 kb) in two mutants (Zmfatb) and eight wild-types (ZmfatB) inbreds to study allelic variation, gene-based diversity, phylogenetic-relationship, protein-modelling, and molecular-docking to identify novel candidates for modification of fatty acid profile. Sequence alignment revealed wide genomic variability for Zmfatb among the inbreds; identified five novel SNPs and two InDels that clearly differentiated the wild-type and mutant genotypes. Gene-based diversity using 11-InDel markers categorised 48-diverse maize-inbreds into two-clusters. The majority of mutant and wild-type inbreds were grouped in separate clusters and led to the generation of 41 haplotypes. Genetic relationship of maize fatb gene with orthologues among 40 accessions of 12 oilseed-crops using both nucleotide and protein sequence clustered maize, soybean, sunflower, opium-poppy, Citrulus lanata, quinoa, and prunus species into one cluster; and brassica, camelina, and arabidopsis into the different cluster. The clustering pattern revealed that the plant oil with higher unsaturated fatty acids, particularly oleic, linoleic, and linolenic acids grouped together in one cluster and higher proportions of other fractions like arachidic, eicosenoic, and erucic acids grouped in another cluster. Physico-chemical properties highlighted more similarity between maize and 29 orthologue proteins, but orthologues were found to have better thermostability. Homology models have been developed for maize mutant and wild-type inbreds using Umbellularia californica (PDB ID: 5x04) as a template. Predicted protein models possessed optimum confidence-score and RMSD values and validated stability via., Ramachandran plots. Molecular docking indicated most of the interactions of protein-ligand were having similar binding-affinity due to the broader specificity of fatty acyl-ACP thioesterases and the presence of conserved-domains across crops. This is the first report on the comprehensive molecular characterisation of the fatb gene in maize and various orthologues. The information generated here provided new insights into the genetic diversity of fatb gene which can be utilised for the enhanced nutritive value of oil in the breeding programme.
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Liu L, Liu T, Tao W, Liao N, Yan Q, Li L, Tan J, Shen W, Cheng H, Sun D. Flavonoids from Scutellaria barbata D. Don exert antitumor activity in colorectal cancer through inhibited autophagy and promoted apoptosis via ATF4/sestrin2 pathway. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 99:154007. [PMID: 35259610 DOI: 10.1016/j.phymed.2022.154007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
PURPOSE Scutellaria barbata D. Don (SB), mainly containing flavonoids, has been frequently used for cancer treatment. However, little research has investigated the antitumor activity of flavonoids from SB (FSB). The current study aimed to assess the antitumor effect of TFSB and elucidate the probable underlying mechanism in vivo and in vitro. STUDY DESIGN FSB was prepared, and its chemical composition was characterized by HPLC-MS. Colorectal HCT116 cells were treated with various concentration of FSB. The viability, proliferation, apoptosis, migration, and autophagy of HCT116 cells were studied, as were further confirmed in tumor xenografts. METHODS Cell viability and proliferation were respectively examined by MTT and EdU staining. ROS was determined with DCFH-DA, and cell apoptosis was detected using flow cytometry. Transwell and wound-healing assays were performed to evaluate cell migration. Immunofluorescence was employed to evaluate sestrin2 and ATF4 level. The protein expressions of p-AMPK, p-ULK1, p-mTOR, 4E-BP1, LC3-I/II, cleaved-caspase-3, Bax, and bcl-2 were investigated by western blot. ATF4 was overexpressed in experiments to explore the role of ATF4/sestrin2 pathway in FSB-mediated efficacy. RESULTS FSB clearly reduced the cell viability, promoted ROS generation, and induced apoptosis in HCT116 cells by down-regulated Bcl-2, and increased cleaved-caspase-3 and Bax. Furthermore, FSB significantly inhibited migration of colorectal cells in a dose-dependent manner. Further mechanistic study indicated that FSB upregulated p-mTOR protein level, and reduced p-AMPK, p-ULK1, p-mTOR, p-4E-BP1 and LC3-I/II expression, which were major autophagy-related genes. In addition, FSB could cause downregulation of endogenous mTOR inhibitor sestrin2 and ATF4 expression. Transient overexpression of ATF4 resulted in mTOR and sestrin2 inhibition, and significantly compromised the effects of FSB on apoptosis and autophagy in HCT116 cells. CONCLUSION Our results reveal, for the first time, that FSB exerts antitumor activity through autophagy inhibition and apoptosis induction via ATF4/sestrin2 pathway in colorectal cancer cells. Scutellaria barbata D. Don may have great potential in the application for the prevention and treatment of human colorectal cancer.
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Affiliation(s)
- Lianfang Liu
- Department of Medical Oncology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou 215600, China; School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Tianya Liu
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Weiwei Tao
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Naikai Liao
- Department of Urology, the First Affiliated Hospital of Guangxi Medical University, Naning 530021, China
| | - Qiuying Yan
- Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine, Nanjing 210023, China
| | - Liu Li
- Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine, Nanjing 210023, China
| | - Jiani Tan
- Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine, Nanjing 210023, China
| | - Weixing Shen
- Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine, Nanjing 210023, China
| | - Haibo Cheng
- Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine, Nanjing 210023, China; Jiangsu Key Laboratory for TCM Formulae Research, Nanjing 210023, China.
| | - Dongdong Sun
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China; Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine, Nanjing 210023, China; Jiangsu Key Laboratory for TCM Formulae Research, Nanjing 210023, China.
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29
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Kang S, Kim KT, Choi J, Kim H, Cheong K, Bandara A, Lee YH. Genomics and Informatics, Conjoined Tools Vital for Understanding and Protecting Plant Health. PHYTOPATHOLOGY 2022; 112:981-995. [PMID: 34889667 DOI: 10.1094/phyto-10-21-0418-rvw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Genomics' impact on crop production continuously expands. The number of sequenced plant and microbial species and strains representing diverse populations of individual species rapidly increases thanks to the advent of next-generation sequencing technologies. Their genomic blueprints revealed candidate genes involved in various functions and processes crucial for crop health and helped in understanding how the sequenced organisms have evolved at the genome level. Functional genomics quickly translates these blueprints into a detailed mechanistic understanding of how such functions and processes work and are regulated; this understanding guides and empowers efforts to protect crops from diverse biotic and abiotic threats. Metagenome analyses help identify candidate microbes crucial for crop health and uncover how microbial communities associated with crop production respond to environmental conditions and cultural practices, presenting opportunities to enhance crop health by judiciously configuring microbial communities. Efficient conversion of disparate types of massive genomics data into actionable knowledge requires a robust informatics infrastructure supporting data preservation, analysis, and sharing. This review starts with an overview of how genomics came about and has quickly transformed life science. We illuminate how genomics and informatics can be applied to investigate various crop health-related problems using selected studies. We end the review by noting why community empowerment via crowdsourcing is crucial to harnessing genomics to protect global food and nutrition security without continuously expanding the environmental footprint of crop production.
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Affiliation(s)
- Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Ki-Tae Kim
- Department of Agricultural Life Science, Sunchon National University, Suncheon 57922, Korea
| | - Jaeyoung Choi
- Korea Institute of Science and Technology Gangneung Institute of Natural Products, Gangneung 25451, Korea
| | - Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Kyeongchae Cheong
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Korea
| | - Ananda Bandara
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Korea
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30
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Nan GL, Teng C, Fernandes J, O'Connor L, Meyers BC, Walbot V. A cascade of bHLH-regulated pathways programs maize anther development. THE PLANT CELL 2022; 34:1207-1225. [PMID: 35018475 PMCID: PMC8972316 DOI: 10.1093/plcell/koac007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 12/20/2021] [Indexed: 05/15/2023]
Abstract
The spatiotemporal development of somatic tissues of the anther lobe is necessary for successful fertile pollen production. This process is mediated by many transcription factors acting through complex, multi-layered networks. Here, our analysis of functional knockout mutants of interacting basic helix-loop-helix genes Ms23, Ms32, basic helix-loop-helix 122 (bHLH122), and bHLH51 in maize (Zea mays) established that male fertility requires all four genes, expressed sequentially in the tapetum (TP). Not only do they regulate each other, but also they encode proteins that form heterodimers that act collaboratively to guide many cellular processes at specific developmental stages. MS23 is confirmed to be the master factor, as the ms23 mutant showed the earliest developmental defect, cytologically visible in the TP, with the most drastic alterations in premeiotic gene expression observed in ms23 anthers. Notably, the male-sterile ms23, ms32, and bhlh122-1 mutants lack 24-nt phased secondary small interfering RNAs (phasiRNAs) and the precursor transcripts from the corresponding 24-PHAS loci, while the bhlh51-1 mutant has wild-type levels of both precursors and small RNA products. Multiple lines of evidence suggest that 24-nt phasiRNA biogenesis primarily occurs downstream of MS23 and MS32, both of which directly activate Dcl5 and are required for most 24-PHAS transcription, with bHLH122 playing a distinct role in 24-PHAS transcription.
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Affiliation(s)
- Guo-Ling Nan
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Chong Teng
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | - John Fernandes
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Lily O'Connor
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
- Department of Biology, Washington University, St Louis, Missouri 63130, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
- The Division of Plant Science and Technology, University of Missouri–Columbia, Columbia, Missouri 65211, USA
- Authors for correspondence: (V.W.) and (B.C.M.)
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, California 94305, USA
- Authors for correspondence: (V.W.) and (B.C.M.)
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31
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Isolation and Molecular Characterisation of TtDro1A and TtDro1B Genes from Triticum turgidum Subspecies durum and turgidum, Study of Their Influences on Seedling Root Angles. PLANTS 2022; 11:plants11060821. [PMID: 35336704 PMCID: PMC8954752 DOI: 10.3390/plants11060821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/01/2022] [Accepted: 03/17/2022] [Indexed: 12/03/2022]
Abstract
Durum wheat (Triticum turgidum, 2n = 4x = AABB) includes several subspecies with differential characteristics in their root system architecture (RSA). Subspecies durum has longer and more vertical roots, while subspecies turgidum has smaller and shallower roots. The homeologous genes TtDro1A and TtDro1B of both subspecies have been identified and found to differ in their sizes, sequences and the proteins they encode. To determine whether there is a relationship between the level of expression of these two genes and the angle adopted by the roots of durum wheat seedlings, their expressions has been studied by RT-qPCR, both in the primary seminal root and in the other seminal roots. The results of the analyses showed that the TtDro1A gene is expressed 1.4 times more in the primary seminal root than in the other seminal roots. Furthermore, this gene is expressed 2.49 to 8.76 times more than TtDro1B depending on root type (primary or seminal) and subspecies. There are positive correlations between the expression ratio of both genes (TtDro1A/TtDro1B) and the mean of all root angles, the most vertical root angle and the most horizontal root angle of the seedlings. The higher the expression of TtDro1B gene, the lower the root growth angles.
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32
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Gardner EJ, Neville MDC, Samocha KE, Barclay K, Kolk M, Niemi MEK, Kirov G, Martin HC, Hurles ME. Reduced reproductive success is associated with selective constraint on human genes. Nature 2022; 603:858-863. [PMID: 35322230 DOI: 10.1038/s41586-022-04549-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 02/07/2022] [Indexed: 12/22/2022]
Abstract
Genome-wide sequencing of human populations has revealed substantial variation among genes in the intensity of purifying selection acting on damaging genetic variants1. Although genes under the strongest selective constraint are highly enriched for associations with Mendelian disorders, most of these genes are not associated with disease and therefore the nature of the selection acting on them is not known2. Here we show that genetic variants that damage these genes are associated with markedly reduced reproductive success, primarily owing to increased childlessness, with a stronger effect in males than in females. We present evidence that increased childlessness is probably mediated by genetically associated cognitive and behavioural traits, which may mean that male carriers are less likely to find reproductive partners. This reduction in reproductive success may account for 20% of purifying selection against heterozygous variants that ablate protein-coding genes. Although this genetic association may only account for a very minor fraction of the overall likelihood of being childless (less than 1%), especially when compared to more influential sociodemographic factors, it may influence how genes evolve over time.
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Affiliation(s)
- Eugene J Gardner
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, UK.,Medical Research Council (MRC) Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Kaitlin E Samocha
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, UK
| | - Kieron Barclay
- Max Planck Institute for Demographic Research, Rostock, Germany.,Demography Unit, Department of Sociology, Stockholm University, Stockholm, Sweden.,Swedish Collegium for Advanced Study, Uppsala, Sweden
| | - Martin Kolk
- Demography Unit, Department of Sociology, Stockholm University, Stockholm, Sweden
| | - Mari E K Niemi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, UK
| | - George Kirov
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Hilary C Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, UK
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, UK.
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33
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Li X, Hou Y, Zhang F, Li M, Yi F, Kang J, Yang Q, Long R. Identification and characterization of stress responsive homeodomain leucine zipper transcription factors in Medicago truncatula. Mol Biol Rep 2022; 49:3569-3581. [PMID: 35118569 DOI: 10.1007/s11033-022-07197-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND Homeodomain leucine zipper (HD-ZIP) transcription factors play roles in regulating plant development and responses to abiotic stresses; however, how HD-ZIP genes in Medicago truncatula are involved in abiotic stress response remains elusive. METHODS AND RESULTS The HD-ZIP I genes in Medicago truncatula were identified and characterized, and their expression patterns in different tissues and under different abiotic stresses were analyzed. A total of 15 Medicago truncatula HD-ZIP I genes were identified and a phylogenetic analysis of HD-ZIP I proteins in Arabidopsis thaliana and Medicago truncatula was conducted. Fifteen HD-ZIP I genes showed diverse tissue preferences. Among them, expressions of MtHB22 and MtHB51 were specially detected in vegetative buds. In addition, they responded to various abiotic stresses, including salinity and osmotic stress and abscisic acid (ABA). For instance, MtHB7 and MtHB12 expression levels were found to be positively associated with salt, osmotic stress and ABA in both shoots and roots, while MtHB13 and MtHB23 were negatively associated with these stresses in Medicago truncatula. CONCLUSION The HD-ZIP I genes in Medicago truncatula are evolutionarily conserved, but also exhibit gene duplication and gene loss events. Differential expression analysis of Medicago truncatula HD-ZIP I genes indicated their crucial roles in abiotic stress responses. Our genome-wide analysis of the HD-ZIP I transcription factor family in Medicago truncatula provided a valuable reference for further research.
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Affiliation(s)
- Xiao Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Yiyao Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Fan Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Mingna Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Fengyan Yi
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, People's Republic of China
| | - Junmei Kang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Ruicai Long
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
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34
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Krzyszton M, Kufel J. Analysis of mRNA-derived siRNAs in mutants of mRNA maturation and surveillance pathways in Arabidopsis thaliana. Sci Rep 2022; 12:1474. [PMID: 35087200 PMCID: PMC8795450 DOI: 10.1038/s41598-022-05574-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/14/2022] [Indexed: 02/05/2023] Open
Abstract
Defects in RNA maturation and RNA decay factors may generate substrates for the RNA interference machinery. This phenomenon was observed in plants where mutations in some RNA-related factors lead to the production of RNA-quality control small interfering RNAs and several mutants show enhanced silencing of reporter transgenes. To assess the potential of RNAi activation on endogenous transcripts, we sequenced small RNAs from a set of Arabidopsis thaliana mutants with defects in various RNA metabolism pathways. We observed a global production of siRNAs caused by inefficient pre-mRNA cleavage and polyadenylation leading to read-through transcription into downstream antisense genes. In addition, in the lsm1a lsm1b double mutant, we identified NIA1, SMXL5, and several miRNA-targeted mRNAs as producing siRNAs, a group of transcripts suggested being especially sensitive to deficiencies in RNA metabolism. However, in most cases, RNA metabolism perturbations do not lead to the widespread production of siRNA derived from mRNA molecules. This observation is contrary to multiple studies based on reporter transgenes and suggests that only a very high accumulation of defective mRNA species caused by specific mutations or substantial RNA processing defects trigger RNAi pathways.
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Affiliation(s)
- Michal Krzyszton
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Joanna Kufel
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
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35
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Newman R, Tolar P. Chronic calcium signaling in IgE + B cells limits plasma cell differentiation and survival. Immunity 2021; 54:2756-2771.e10. [PMID: 34879220 DOI: 10.1016/j.immuni.2021.11.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/30/2021] [Accepted: 11/12/2021] [Indexed: 01/28/2023]
Abstract
In contrast to other antibody isotypes, B cells switched to IgE respond transiently and do not give rise to long-lived plasma cells (PCs) or memory B cells. To better understand IgE-BCR-mediated control of IgE responses, we developed whole-genome CRISPR screening that enabled comparison of IgE+ and IgG1+ B cell requirements for proliferation, survival, and differentiation into PCs. IgE+ PCs exhibited dependency on the PI3K-mTOR axis that increased protein amounts of the transcription factor IRF4. In contrast, loss of components of the calcium-calcineurin-NFAT pathway promoted IgE+ PC differentiation. Mice bearing a B cell-specific deletion of calcineurin B1 exhibited increased production of IgE+ PCs. Mechanistically, sustained elevation of intracellular calcium in IgE+ PCs downstream of the IgE-BCR promoted BCL2L11-dependent apoptosis. Thus, chronic calcium signaling downstream of the IgE-BCR controls the self-limiting character of IgE responses and may be relevant to the accumulation of IgE-producing cells in allergic disease.
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Affiliation(s)
- Rebecca Newman
- Immune Receptor Activation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Pavel Tolar
- Immune Receptor Activation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London NW3 2PF, UK.
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36
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Golisz A, Krzyszton M, Stepien M, Dolata J, Piotrowska J, Szweykowska-Kulinska Z, Jarmolowski A, Kufel J. Arabidopsi s Spliceosome Factor SmD3 Modulates Immunity to Pseudomonas syringae Infection. FRONTIERS IN PLANT SCIENCE 2021; 12:765003. [PMID: 34925413 PMCID: PMC8678131 DOI: 10.3389/fpls.2021.765003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/11/2021] [Indexed: 06/02/2023]
Abstract
SmD3 is a core component of the small nuclear ribonucleoprotein (snRNP) that is essential for pre-mRNA splicing. The role of Arabidopsis SmD3 in plant immunity was assessed by testing sensitivity of smd3a and smd3b mutants to Pseudomonas syringae pv. tomato (Pst) DC3000 infection and its pathogenesis effectors flagellin (flg22), EF-Tu (elf18) and coronatine (COR). Both smd3 mutants exhibited enhanced susceptibility to Pst accompanied by marked changes in the expression of key pathogenesis markers. mRNA levels of major biotic stress response factors were also altered upon treatment with Pseudomonas effectors. Our genome-wide transcriptome analysis of the smd3b-1 mutant infected with Pst, verified by northern and RT-qPCR, showed that lack of SmD3-b protein deregulates defense against Pst infection at the transcriptional and posttranscriptional levels including defects in splicing and an altered pattern of alternative splicing. Importantly, we show that SmD3-b dysfunction impairs mainly stomatal immunity as a result of defects in stomatal development. We propose that it is the malfunction of the stomata that is the primary cause of an altered mutant response to the pathogen. Other changes in the smd3b-1 mutant involved enhanced elf18- and flg22-induced callose deposition, reduction of flg22-triggered production of early ROS and boost of secondary ROS caused by Pst infection. Together, our data indicate that SmD3 contributes to the plant immune response possibly via regulation of mRNA splicing of key pathogenesis factors.
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Affiliation(s)
- Anna Golisz
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Michal Krzyszton
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Monika Stepien
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Jakub Dolata
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Justyna Piotrowska
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna Kufel
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
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37
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Chen H, Wang Y, Liu J, Zhao T, Yang C, Ding Q, Zhang Y, Mu J, Wang D. Identification of WRKY transcription factors responding to abiotic stresses in Brassica napus L. PLANTA 2021; 255:3. [PMID: 34837557 DOI: 10.1007/s00425-021-03733-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
A total of 278 BnWRKYs were identified and analyzed. Ectopic expression of BnWRKY149 and BnWRKY217 suggests that they function in the ABA signaling pathway. WRKY transcription factors play an important role in plant development, however, their function in Brassica napus L. abiotic stress response is still unclear. In this study, a total of 278 BnWRKY transcription factors were identified from the B. napus genome data, and they were subsequently distributed in three main groups. The protein motifs and classification of BnWRKY transcription factors were analyzed, and the locations of their corresponding encoding genes were mapped on the chromosomes of B. napus. Transcriptome analysis of rapeseed seedlings exposed to drought, salt, heat, cold and abscisic acid treatment revealed that 99 BnWRKYs responded to at least one of these stresses. The expression profiles of 12 BnWRKYs were examined with qPCR and the result coincided with RNA-seq analysis. Two genes of interest, BnWRKY149 and BnWRKY217 (homologs of AtWRKY40), were overexpressed in Arabidopsis, and the corresponding proteins were located to the nucleus. Transgene plants of BnWRKY149 and BnWRKY217 were less sensitive to ABA than Arabidopsis Col-0 plants, suggesting they might play important roles in the responses of rapeseed to abiotic stress.
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Affiliation(s)
- Hao Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Yongfeng Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Jiong Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Tian Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Cuiling Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Qunying Ding
- School of Biological and Environmental Engineering, Xi'an University, Xi'an, 710065, Shaanxi, China
| | - Yanfeng Zhang
- Hybrid Rapeseed Research Center of Shanxi Province, Yangling, 712100, Shaanxi, China
| | - Jianxin Mu
- Hybrid Rapeseed Research Center of Shanxi Province, Yangling, 712100, Shaanxi, China
| | - DaoJie Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China.
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38
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Nguyen NTT, Vincens P, Dufayard JF, Roest Crollius H, Louis A. Genomicus in 2022: comparative tools for thousands of genomes and reconstructed ancestors. Nucleic Acids Res 2021; 50:D1025-D1031. [PMID: 34792170 PMCID: PMC8728260 DOI: 10.1093/nar/gkab1091] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 11/30/2022] Open
Abstract
Genomicus is a database and web-server dedicated to comparative genomics in eukaryotes. Its main functionality is to graphically represent the conservation of genomic blocks between multiple genomes, locally around a specific gene of interest or genome-wide through karyotype comparisons. Since 2010 and its first release, Genomicus has synchronized with 60 Ensembl releases and seen the addition of functions that have expanded the type of analyses that users can perform. Today, five public instances of Genomicus are supporting a total number of 1029 extant genomes and 621 ancestral reconstructions from all eukaryotes kingdoms available in Ensembl and Ensembl Genomes databases complemented with four additional instances specific to taxonomic groups of interest. New visualization and query tools are described in this manuscript. Genomicus is freely available at http://www.genomicus.bio.ens.psl.eu/genomicus.
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Affiliation(s)
- Nga Thi Thuy Nguyen
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Pierre Vincens
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Jean François Dufayard
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France - UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France.,French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Hugues Roest Crollius
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Alexandra Louis
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
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39
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Telzrow CL, Zwack PJ, Esher Righi S, Dietrich FS, Chan C, Owzar K, Alspaugh JA, Granek JA. Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries. G3 (BETHESDA, MD.) 2021; 11:jkab301. [PMID: 34518880 PMCID: PMC8527493 DOI: 10.1093/g3journal/jkab301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 08/19/2021] [Indexed: 11/13/2022]
Abstract
RNA sequencing (RNA-Seq) experiments focused on gene expression involve removal of ribosomal RNA (rRNA) because it is the major RNA constituent of cells. This process, called RNA enrichment, is done primarily to reduce cost: without rRNA removal, deeper sequencing must be performed to compensate for the sequencing reads wasted on rRNA. The ideal RNA enrichment method removes all rRNA without affecting other RNA in the sample. We tested the performance of three RNA enrichment methods on RNA isolated from Cryptococcus neoformans, a fungal pathogen of humans. We find that the RNase H depletion method is more efficient in depleting rRNA and more specific in recapitulating non-rRNA levels present in unenriched controls than the commonly-used Poly(A) isolation method. The RNase H depletion method is also more effective than the Ribo-Zero depletion method as measured by rRNA depletion efficiency and recapitulation of protein-coding RNA levels present in unenriched controls, while the Ribo-Zero depletion method more closely recapitulates annotated non-coding RNA (ncRNA) levels. Finally, we leverage these data to accurately map the C. neoformans mitochondrial rRNA genes, and also demonstrate that RNA-Seq data generated with the RNase H and Ribo-Zero depletion methods can be used to explore novel C. neoformans long non-coding RNA genes.
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Affiliation(s)
- Calla L Telzrow
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Paul J Zwack
- Department of Biology, Duke University, Durham, NC 27710, USA
| | - Shannon Esher Righi
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Fred S Dietrich
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
- Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - J Andrew Alspaugh
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joshua A Granek
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
- Duke Cancer Institute, Duke University, Durham, NC 27710, USA
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40
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Malla KB, Thapa G, Doohan FM. Mitochondrial phosphate transporter and methyltransferase genes contribute to Fusarium head blight Type II disease resistance and grain development in wheat. PLoS One 2021; 16:e0258726. [PMID: 34648604 PMCID: PMC8516198 DOI: 10.1371/journal.pone.0258726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 10/04/2021] [Indexed: 11/18/2022] Open
Abstract
Fusarium head blight (FHB) is an economically important disease of wheat that results in yield loss and grain contaminated with fungal mycotoxins that are harmful to human and animal health. Herein we characterised two wheat genes involved in the FHB response in wheat: a wheat mitochondrial phosphate transporter (TaMPT) and a methyltransferase (TaSAM). Wheat has three sub-genomes (A, B, and D) and gene expression studies demonstrated that TaMPT and TaSAM homoeologs were differentially expressed in response to FHB infection and the mycotoxigenic Fusarium virulence factor deoxynivalenol (DON) in FHB resistant wheat cv. CM82036 and susceptible cv. Remus. Virus-induced gene silencing (VIGS) of either TaMPT or TaSAM enhanced the susceptibility of cv. CM82036 to FHB disease, reducing disease spread (Type II disease resistance). VIGS of TaMPT and TaSAM significantly reduced grain number and grain weight. This indicates TaSAM and TaMPT genes also contribute to grain development in wheat and adds to the increasing body of evidence linking FHB resistance genes to grain development. Hence, Fusarium responsive genes TaSAM and TaMPT warrant further study to determine their potential to enhance both disease resistance and grain development in wheat.
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Affiliation(s)
- Keshav B. Malla
- UCD Earth Institute, UCD Institute of Food and Health and UCD School of Biology and Environmental Sciences, UCD Science Centre East, University College Dublin, Belfield, Dublin, Ireland
| | - Ganesh Thapa
- UCD Earth Institute, UCD Institute of Food and Health and UCD School of Biology and Environmental Sciences, UCD Science Centre East, University College Dublin, Belfield, Dublin, Ireland
| | - Fiona M. Doohan
- UCD Earth Institute, UCD Institute of Food and Health and UCD School of Biology and Environmental Sciences, UCD Science Centre East, University College Dublin, Belfield, Dublin, Ireland
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41
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Goh W, Mutwil M. LSTrAP-Kingdom: an automated pipeline to generate annotated gene expression atlases for kingdoms of life. Bioinformatics 2021; 37:3053-3055. [PMID: 33704421 DOI: 10.1093/bioinformatics/btab168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/26/2021] [Accepted: 03/08/2021] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION There are now more than two million RNA sequencing experiments for plants, animals, bacteria and fungi publicly available, allowing us to study gene expression within and across species and kingdoms. However, the tools allowing the download, quality control and annotation of this data for more than one species at a time are currently missing. RESULTS To remedy this, we present the Large-Scale Transcriptomic Analysis Pipeline in Kingdom of Life (LSTrAP-Kingdom) pipeline, which we used to process 134 521 RNA-seq samples, achieving ∼12 000 processed samples per day. Our pipeline generated quality-controlled, annotated gene expression matrices that rival the manually curated gene expression data in identifying functionally related genes. AVAILABILITY AND IMPLEMENTATION LSTrAP-Kingdom is available from: https://github.com/wirriamm/plants-pipeline and is fully implemented in Python and Bash. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- William Goh
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore
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Johnson-Weaver BT, Choi HW, Yang H, Granek JA, Chan C, Abraham SN, Staats HF. Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit Immunogens. Front Immunol 2021; 12:730346. [PMID: 34566991 PMCID: PMC8461742 DOI: 10.3389/fimmu.2021.730346] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/23/2021] [Indexed: 01/02/2023] Open
Abstract
Mast cell activators are a novel class of mucosal vaccine adjuvants. The polymeric compound, Compound 48/80 (C48/80), and cationic peptide, Mastoparan 7 (M7) are mast cell activators that provide adjuvant activity when administered by the nasal route. However, small molecule mast cell activators may be a more cost-efficient adjuvant alternative that is easily synthesized with high purity compared to M7 or C48/80. To identify novel mast cell activating compounds that could be evaluated for mucosal vaccine adjuvant activity, we employed high-throughput screening to assess over 55,000 small molecules for mast cell degranulation activity. Fifteen mast cell activating compounds were down-selected to five compounds based on in vitro immune activation activities including cytokine production and cellular cytotoxicity, synthesis feasibility, and selection for functional diversity. These small molecule mast cell activators were evaluated for in vivo adjuvant activity and induction of protective immunity against West Nile Virus infection in BALB/c mice when combined with West Nile Virus envelope domain III (EDIII) protein in a nasal vaccine. We found that three of the five mast cell activators, ST101036, ST048871, and R529877, evoked high levels of EDIII-specific antibody and conferred comparable levels of protection against WNV challenge. The level of protection provided by these small molecule mast cell activators was comparable to the protection evoked by M7 (67%) but markedly higher than the levels seen with mice immunized with EDIII alone (no adjuvant 33%). Thus, novel small molecule mast cell activators identified by high throughput screening are as efficacious as previously described mast cell activators when used as nasal vaccine adjuvants and represent next-generation mast cell activators for evaluation in mucosal vaccine studies.
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Affiliation(s)
| | - Hae Woong Choi
- Pathology Department, School of Medicine, Duke University, Durham, NC, United States
| | - Hang Yang
- Biostatistics and Bioinformatics Department, School of Medicine, Duke University, Durham, NC, United States
| | - Josh A. Granek
- Biostatistics and Bioinformatics Department, School of Medicine, Duke University, Durham, NC, United States
| | - Cliburn Chan
- Biostatistics and Bioinformatics Department, School of Medicine, Duke University, Durham, NC, United States
| | - Soman N. Abraham
- Pathology Department, School of Medicine, Duke University, Durham, NC, United States
- Department of Immunology, School of Medicine, Duke University, Durham, NC, United States
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, United States
| | - Herman F. Staats
- Pathology Department, School of Medicine, Duke University, Durham, NC, United States
- Department of Immunology, School of Medicine, Duke University, Durham, NC, United States
- Duke Human Vaccine Institute, Duke University, Durham, NC, United States
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43
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Fukuda A, Hirose T, Hashida Y, Aoki N, Nagano AJ. Selection of transcripts related to low-temperature tolerance using RNA sequencing from F 2 plants between japonica and indica rice (Oryza sativa L.) cultivars. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:984-993. [PMID: 34112311 DOI: 10.1071/fp21088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
At low temperatures (18°C), seedlings of an indica rice (Oryza sativa L.) cultivar Kasalath showed symptoms of chlorosis, although the leaves of a japonica cultivar Arroz da Terra remained green. In this study, transcripts related to the chlorophyll content of rice seedlings grown at 18°C were investigated using RNA-sequencing (RNA-Seq) data for F2 crosses between cultivars Arroz da Terra and Kasalath, as well as their parental cultivars. Differential expression analysis revealed that gene ontology terms related to 'photosynthesis' were significantly enriched in lowly expressed genes at 18°C than at 25°C in Kasalath. However, the gene ontology terms related to 'response to stress' were significantly enriched in highly expressed genes at 18°C than at 25°C in Kasalath. When the F2 plants were grown at 18°C, their chlorophyll contents varied. Transcripts with expression levels related to chlorophyll content were statistically selected using RNA-Seq data from 21 F2 plants. In regression models, frequently selected genes included four photosynthetic and two stress-responsive genes. The expression values of four photosynthetic and two stress-responsive genes in high-frequency selected genes were significantly correlated with chlorophyll content not only in plants analysed using RNA-Seq but also in 95 F2 plants.
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Affiliation(s)
- Akari Fukuda
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan; and Corresponding author.
| | - Tatsuro Hirose
- Faculty of Agriculture, Takasaki University of Health and Welfare, Takasaki, Gunma, Japan
| | - Yoichi Hashida
- Faculty of Agriculture, Takasaki University of Health and Welfare, Takasaki, Gunma, Japan
| | - Naohiro Aoki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Lee YW, Chen M, Chung IF, Chang TY. lncExplore: a database of pan-cancer analysis and systematic functional annotation for lncRNAs from RNA-sequencing data. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6360505. [PMID: 34464437 PMCID: PMC8407485 DOI: 10.1093/database/baab053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 06/18/2021] [Accepted: 08/10/2021] [Indexed: 12/23/2022]
Abstract
Over the past few years, with the rapid growth of deep-sequencing technology and the development of computational prediction algorithms, a large number of long non-coding RNAs (lncRNAs) have been identified in various types of human cancers. Therefore, it has become critical to determine how to properly annotate the potential function of lncRNAs from RNA-sequencing (RNA-seq) data and arrange the robust information and analysis into a useful system readily accessible by biological and clinical researchers. In order to produce a collective interpretation of lncRNA functions, it is necessary to integrate different types of data regarding the important functional diversity and regulatory role of these lncRNAs. In this study, we utilized transcriptomic sequencing data to systematically observe and identify lncRNAs and their potential functions from 5034 The Cancer Genome Atlas RNA-seq datasets covering 24 cancers. Then, we constructed the 'lncExplore' database that was developed to comprehensively integrate various types of genomic annotation data for collective interpretation. The distinctive features in our lncExplore database include (i) novel lncRNAs verified by both coding potential and translation efficiency score, (ii) pan-cancer analysis for studying the significantly aberrant expression across 24 human cancers, (iii) genomic annotation of lncRNAs, such as cis-regulatory information and gene ontology, (iv) observation of the regulatory roles as enhancer RNAs and competing endogenous RNAs and (v) the findings of the potential lncRNA biomarkers for the user-interested cancers by integrating clinical information and disease specificity score. The lncExplore database is to our knowledge the first public lncRNA annotation database providing cancer-specific lncRNA expression profiles for not only known but also novel lncRNAs, enhancer RNAs annotation and clinical analysis based on pan-cancer analysis. lncExplore provides a more complete pathway to highly efficient, novel and more comprehensive translation of laboratory discoveries into the clinical context and will assist in reinterpreting the biological regulatory function of lncRNAs in cancer research. Database URL http://lncexplore.bmi.nycu.edu.tw.
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Affiliation(s)
- Yi-Wei Lee
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, No.155, Sec. 2, Linong St., Beitou District, Taipei 11221, Taiwan
| | - Ming Chen
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, No.176, Chong-Hua Rd., Changhua 50046, Taiwan.,Research Department, Changhua Christian Hospital, No.135, Nan-Hsiao St., Changhua 50006, Taiwan.,Department of Genomic Science and Technology, Changhua Christian Hospital Healthcare System, No.176, Chong-Hua Rd., Changhua 50046, Taiwan.,Department of Obstetrics and Gynecology, Changhua Christian Hospital, No.135, Nan-Hsiao St., Changhua 50006, Taiwan.,Department of Medical Genetics, National Taiwan University Hospital, No.7, Chung Shan S. Rd.(Zhongshan S. Rd.), Zhongzheng Dist., Taipei 10041, Taiwan.,Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, No.7, Chung Shan S. Rd.(Zhongshan S. Rd.), Zhongzheng Dist., Taipei 10041, Taiwan.,Department of Biomedical Science, Dayeh University, No.168, University Rd., Dacun, Changhua 51591, Taiwan.,Department of Medical Science, National Tsing Hua University, No.101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - I-Fang Chung
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, No.155, Sec. 2, Linong St., Beitou District, Taipei 11221, Taiwan.,Center for Systems and Synthetic Biology, National Yang Ming Chiao Tung University, No.155, Sec. 2, Linong St., Beitou District, Taipei 11221, Taiwan
| | - Ting-Yu Chang
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, No.176, Chong-Hua Rd., Changhua 50046, Taiwan.,Research Department, Changhua Christian Hospital, No.135, Nan-Hsiao St., Changhua 50006, Taiwan.,Department of Genomic Science and Technology, Changhua Christian Hospital Healthcare System, No.176, Chong-Hua Rd., Changhua 50046, Taiwan.,Department of Bioscience Technology, Chung Yuan Christian University, No.200, Chung Pei Road, Chung Li District, Taoyuan 32023, Taiwan
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45
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Xu BH, Jiang JH, Luo T, Jiang ZJ, Liu XY, Li LQ. Signature of prognostic epithelial-mesenchymal transition related long noncoding RNAs (ERLs) in hepatocellular carcinoma. Medicine (Baltimore) 2021; 100:e26762. [PMID: 34397721 PMCID: PMC8322489 DOI: 10.1097/md.0000000000026762] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/04/2021] [Indexed: 01/04/2023] Open
Abstract
Reliable biomarkers are of great significance for the treatment and diagnosis of hepatocellular carcinoma (HCC). This study identified potential prognostic epithelial-mesenchymal transition related lncRNAs (ERLs) by the cancer genome atlas (TCGA) database and bioinformatics.The differential expression of long noncoding RNA (lncRNA) was obtained by analyzing the lncRNA data of 370 HCC samples in TCGA. Then, Pearson correlation analysis was carried out with EMT related genes (ERGs) from molecular signatures database. Combined with the univariate Cox expression analysis of the total survival rate of hepatocellular carcinoma (HCC) patients, the prognostic ERLs were obtained. Then use "step" function to select the optimal combination of constructing multivariate Cox expression model. The expression levels of ERLs in HCC samples were verified by real-time quantitative polymerase chain reaction.Finally, we identified 5 prognostic ERLs (AC023157.3, AC099850.3, AL031985.3, AL365203.2, CYTOR). The model showed that these prognostic markers were reliable independent predictors of risk factors (P value <.0001, hazard ratio [HR] = 2.400, 95% confidence interval [CI] = 1.667-3.454 for OS). In the time-dependent receiver operating characteristic analysis, this prognostic marker is a good predictor of HCC survival (area under the curve of 1 year, 2 years, 3 years, and 5 years are 0.754, 0.720, 0.704, and 0.662 respectively). We analyzed the correlation of clinical characteristics of these prognostic markers, and the results show that this prognostic marker is an independent factor that can predict the prognosis of HCC more accurately. In addition, by matching with the Molecular Signatures Database, we obtained 18 ERLs, and then constructed the HCC prognosis model and clinical feature correlation analysis using 5 prognostic ERLs. The results show that these prognostic markers have reliable independent predictive value. Bioinformatics analysis showed that these prognostic markers were involved in the regulation of EMT and related functions of tumor occurrence and migration.Five prognostic types of ERLs identified in this study can be used as potential biomarkers to predict the prognosis of HCC.
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Affiliation(s)
- Bang-Hao Xu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jing-Hang Jiang
- Department of Hepatobiliary Surgery, Jing Men NO.2 People's Hospital, Jingmen, Hubei, China
| | - Tao Luo
- Department of Hepatobiliary Surgery, Guangxi Medical University Affiliated Tumor Hospital, Nanning, Guangxi, China
| | - Zhi-Jun Jiang
- Department of Hepatobiliary Surgery, Guangxi Medical University Affiliated Tumor Hospital, Nanning, Guangxi, China
| | - Xin-Yu Liu
- Department of Hepatobiliary Surgery, Guangxi Medical University Affiliated Tumor Hospital, Nanning, Guangxi, China
| | - Le-Qun Li
- Department of Hepatobiliary Surgery, Guangxi Medical University Affiliated Tumor Hospital, Nanning, Guangxi, China
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46
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Basunia MA, Nonhebel HM, Backhouse D, McMillan M. Localised expression of OsIAA29 suggests a key role for auxin in regulating development of the dorsal aleurone of early rice grains. PLANTA 2021; 254:40. [PMID: 34324072 DOI: 10.1007/s00425-021-03688-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Non-canonical AUX/IAA protein, OsIAA29, and ZmMPR-1 homologues, OsMRPLs, are part of an auxin-related signalling cascade operating in the dorsal aleurone during early rice grain development. Endosperm of rice and other cereals accumulates high concentrations of the predominant in planta auxin, indole-3-acetic acid (IAA) during early grain development. However, IAA signalling and function during endosperm development are poorly understood. Here, we report that OsYUC12 (an auxin biosynthesis gene) and OsIAA29 (encoding a non-canonical AUX/IAA) are both expressed exclusively in grains, reaching a maximum 5-6 days after pollination. OsYUC12 expression is localised in the aleurone, sub-aleurone and embryo, whereas OsIAA29 expression is restricted to a narrow strip in the dorsal aleurone, directly under the vascular bundle. Although rice has been reported to lack endosperm transfer cells (ETCs), this region of the aleurone is enriched with sugar transporters and is likely to play a key role in apoplastic nutrient transfer, analogous to ETCs in other cereals. OsIAA29 has orthologues only in grass species; expression of which is also specific to early grain development. OsYUC12 and OsIAA29 are temporally co-expressed with two genes (AL1 and OsPR602) previously linked to the development of dorsal aleurone or ETCs. Also up-regulated at the same time is a cluster of MYB-related genes (designated OsMRPLs) homologous to ZmMRP-1, which regulates maize ETC development. Wheat homologues of ZmMRP-1 are similarly expressed in ETCs. Although previous work has suggested that other cereals do not have orthologues of ZmMRP-1, our work suggests OsIAA29 and OsMRPLs and their homologues in other grasses are part of an auxin-regulated, conserved signalling network involved in the differentiation of cells with ETC-like function in developing cereal grains.
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Affiliation(s)
- Mafroz A Basunia
- School of Science and Technology, University of New England, Armidale, NSW, 2351, Australia
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Dhaka, 1342, Bangladesh
| | - Heather M Nonhebel
- School of Science and Technology, University of New England, Armidale, NSW, 2351, Australia.
| | - David Backhouse
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Mary McMillan
- School of Science and Technology, University of New England, Armidale, NSW, 2351, Australia
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47
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Kabir MR, Nonhebel HM. Reinvestigation of THOUSAND-GRAIN WEIGHT 6 grain weight genes in wheat and rice indicates a role in pollen development rather than regulation of auxin content in grains. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2051-2062. [PMID: 33687498 DOI: 10.1007/s00122-021-03804-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
Phylogenetic and expression analyses of grain weight genes TaTGW6 and OsTGW6 and investigation of substrate availability indicate TGW6 does not regulate auxin content of grains but may affect pollen development. The THOUSAND-GRAIN WEIGHT 6 genes (TaTGW6 and OsTGW6) are reported to result in larger grains of wheat and rice by reducing production of indole-3-acetic acid (IAA) in developing grains. However, a critical comparison of data on TaTGW6 and OsTGW6 with other reports on IAA synthesis in cereal grains requires that this hypothesis be reinvestigated. Here, we show that TaTGW6 and OsTGW6 are members of a large gene family that has undergone major, lineage-specific gene expansion. Wheat has nine genes, and rice three genes encoding proteins with more than 80% amino acid identity with TGW6, making it difficult to envisage how a single inactive allele could have a major effect on IAA levels in grains. In our study, we show that neither TaTGW6 nor OsTGW6 is expressed in developing grains. Instead, both genes and their close homologues are exclusively expressed in pre-emergent inflorescences; TaTGW6 is expressed particularly in microspores prior to mitosis. This evidence, combined with our observation that developing wheat grains have undetectable levels of ester IAA in comparison to free IAA and do not express an IAA-glucose synthase suggests that TaTGW6 and OsTGW6 do not regulate grain size via the hydrolysis of IAA-glucose. Instead, their similarity to rice strictosidine synthase-like (OsSTRL2) suggests they play a key role in pollen development.
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Affiliation(s)
- Muhammed Rezwan Kabir
- School of Science and Technology, University of New England, Armidale, NSW, 2351, Australia
| | - Heather M Nonhebel
- School of Science and Technology, University of New England, Armidale, NSW, 2351, Australia.
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48
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Kabir MR, Nonhebel HM, Backhouse D, Winter G. Expression of key auxin biosynthesis genes correlates with auxin and starch content of developing wheat (Triticum aestivum) grains. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:802-814. [PMID: 33715766 DOI: 10.1071/fp20319] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
The effect of auxin on wheat (Triticum aestivum L.) grain size is contentious. Additionally, the contributions to the IAA pool from de novo synthesis versus hydrolysis of IAA-glucose are unclear. Here, we describe the first comprehensive study of tryptophan aminotransferase and indole-3-pyruvate mono-oxygenase expression from 5 to 20 days after anthesis. A comparison of expression data with measurements of endogenous IAA via combined liquid chromatography-tandem mass spectrometry using heavy isotope labelled internal standards indicates that TaTAR2-B3, TaYUC9-A1, TaYUC9-B, TaYUC9-D1, TaYUC10-A and TaYUC10-D are primarily responsible for IAA production in developing grains. Furthermore, these genes are expressed specifically in developing grains, like those found in rice (Oryza sativa L.) and maize (Zea mays L.). Our results cast doubt on the proposed role of THOUSAND-GRAIN WEIGHT gene, TaTGW6, in promoting larger grain size via negative effects on grain IAA content. Work on this gene overlooked the contribution of IAA biosynthesis from tryptophan. Although IAA synthesis occurs primarily in the endosperm, we show the TaYUC9-1 group is also strongly expressed in the embryo. Within the endosperm, TaYUC9-1 expression is highest in aleurone and transfer cells, suggesting that IAA has a key role in differentiation of these tissues as has been proposed for other cereals.
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Affiliation(s)
- Muhammed Rezwan Kabir
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
| | - Heather M Nonhebel
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia; and Corresponding author.
| | - David Backhouse
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Gal Winter
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
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Chhabra R, Muthusamy V, Gain N, Katral A, Prakash NR, Zunjare RU, Hossain F. Allelic variation in sugary1 gene affecting kernel sweetness among diverse-mutant and -wild-type maize inbreds. Mol Genet Genomics 2021; 296:1085-1102. [PMID: 34159441 DOI: 10.1007/s00438-021-01807-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/16/2021] [Indexed: 12/01/2022]
Abstract
Sweet corn is popular worldwide as vegetable. Though large numbers of sugary1 (su1)-based sweet corn germplasm are available, allelic diversity in su1 gene encoding SU1 isoamylase among diverse maize inbreds has not been analyzed. Here, we characterized the su1 gene in maize and compared with allied species. The entire su1 gene (11,720 bp) was sequenced among six mutant (su1) and five wild (Su1) maize inbreds. Fifteen InDels of 2-45 bp were selected to develop markers for studying allelic diversity in su1 gene among 19 mutant- (su1) and 29 wild-type (Su1) inbreds. PIC ranged from 0.15 (SU-InDel7) to 0.37 (SU-InDel13). Major allele frequency varied from 0.52 to 0.90, while gene diversity ranged from 0.16 to 0.49. Phylogenetic tree categorized 48 maize inbreds in two clusters each for wild- type (Su1) and mutant (su1) types. 44 haplotypes of su1 were observed, with three haplotypes (Hap6, Hap22 and Hap29) sharing more than one genotype. Further, comparisons were made with 23 orthologues of su1 from 16 grasses and Arabidopsis. Maize possessed 15-19 exons in su1, while it was 11-24 exons among orthologues. Introns among the orthologues were longer (77-2206 bp) than maize (859-1718 bp). SU1 protein of maize and orthologues had conserved α-amylase and CBM_48 domains. The study also provided physicochemical properties and secondary structure of SU1 protein in maize and its orthologues. Phylogenetic analysis showed closer relationship of maize SU1 protein with P. hallii, S. bicolor and E. tef than Triticum sp. and Oryza sp. The study showed that presence of high allelic diversity in su1 gene which can be utilized in the sweet corn breeding program. This is the first report of comprehensive characterization of su1 gene and its allelic forms in diverse maize and related orthologues.
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Affiliation(s)
- Rashmi Chhabra
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vignesh Muthusamy
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Nisrita Gain
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Nitish R Prakash
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Firoz Hossain
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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50
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Browne RG, Li SF, Iacuone S, Dolferus R, Parish RW. Differential responses of anthers of stress tolerant and sensitive wheat cultivars to high temperature stress. PLANTA 2021; 254:4. [PMID: 34131818 DOI: 10.1007/s00425-021-03656-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 06/03/2021] [Indexed: 05/27/2023]
Abstract
Transcriptomic analyses identified anther-expressed genes in wheat likely to contribute to heat tolerance and hence provide useful genetic markers. The genes included those involved in hormone biosynthesis, signal transduction, the heat shock response and anther development. Pollen development is particularly sensitive to high temperature heat stress. In wheat, heat-tolerant and heat-sensitive cultivars have been identified, although the underlying genetic causes for these differences are largely unknown. The effects of heat stress on the developing anthers of two heat-tolerant and two heat-sensitive wheat cultivars were examined in this study. Heat stress (35 °C) was found to disrupt pollen development in the two heat-sensitive wheat cultivars but had no visible effect on pollen or anther development in the two heat-tolerant cultivars. The sensitive anthers exhibited a range of developmental abnormalities including an increase in unfilled and clumped pollen grains, abnormal pollen walls and a decrease in pollen viability. This subsequently led to a greater reduction in grain yield in the sensitive cultivars following heat stress. Transcriptomic analyses of heat-stressed developing wheat anthers of the four cultivars identified a number of key genes which may contribute to heat stress tolerance during pollen development. Orthologs of some of these genes in Arabidopsis and rice are involved in regulation of the heat stress response and the synthesis of auxin, ethylene and gibberellin. These genes constitute candidate molecular markers for the breeding of heat-tolerant wheat lines.
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Affiliation(s)
- Richard G Browne
- AgriBio, Centre for Agribioscience, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Song F Li
- AgriBio, Centre for Agribioscience, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Sylvana Iacuone
- AgriBio, Centre for Agribioscience, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
- Melbourne Polytechnic, Epping, VIC, Australia
| | - Rudy Dolferus
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Roger W Parish
- AgriBio, Centre for Agribioscience, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia.
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