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Chibani S, Yacoub E, Boujemaa S, Mardassi H, Guglielmini J, Vaysse A, Khadraoui N, Mlik B, Ben Abdelmoumen Mardassi B. A genome-wide investigation of Mycoplasma hominis genes associated with gynecological infections or infertility. Front Microbiol 2025; 16:1561378. [PMID: 40371111 PMCID: PMC12075135 DOI: 10.3389/fmicb.2025.1561378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Accepted: 03/18/2025] [Indexed: 05/16/2025] Open
Abstract
Background and aim Mycoplasma hominis is a human pathogenic bacterium that causes a wide range of genital infections and reproductive issues. Previously, based on an extended multilocus sequence typing scheme, we provided evidence for the segregation of M. hominis clinical strains into two distinct pathotypes: gynecological infections or infertility. Here, based on whole genome sequencing (WGS) data, we sought to provide a more refined picture of the phylogenetic relationship between these two M. hominis pathotypes, with the aim to delineate the underlying genetic determinants. Methods We carried out WGS of 62 Tunisian M. hominis clinical strains collected over a 17-year period. The majority of these clinical strains are associated with infertility (n = 53) and the remaining nine isolates are from gynecological infections cases. An alignment-free distance-based procedure (Jolytree) was used to infer phylogenetic relationships among M. hominis isolates, while the phylogenetic method treeWAS was used to determine the statistical association between pathotypes of interest and genotypes at all loci. Results The total pangenome of M. hominis strains was found to contain 1,590 genes including 966 core genes and 592 accessory genes, representing 60 and 37% of the total genome, respectively. Collectively, phylogenetic analyses based on WGS confirmed the distinction between the two M. hominis pathotypes. Strikingly, genome wide association analyses identified 4 virulence genes associated with gynecological infections, mainly involved in nucleotide salvage pathways and tolerance to oxidative stress, while five genes have been associated with infertility cases, two of which are implicated in biofilm formation. Conclusion In sum, this study further established the categorization of M. hominis into two pathotypes, and led to the identification of the associated genetic loci, thus holding out promising prospects for a better understanding of the differential interaction of M. hominis with its host.
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Affiliation(s)
- Salim Chibani
- Group of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnological Development, Pasteur Institute of Tunis, University of Tunis-El Manar, Tunis, Tunisia
| | - Elhem Yacoub
- Group of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnological Development, Pasteur Institute of Tunis, University of Tunis-El Manar, Tunis, Tunisia
| | - Safa Boujemaa
- Group of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnological Development, Pasteur Institute of Tunis, University of Tunis-El Manar, Tunis, Tunisia
| | - Helmi Mardassi
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Pasteur Institute of Tunis, University of Tunis-El Manar, Tunis, Tunisia
| | - Julien Guglielmini
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Amaury Vaysse
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Nadine Khadraoui
- Group of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnological Development, Pasteur Institute of Tunis, University of Tunis-El Manar, Tunis, Tunisia
| | - Béhija Mlik
- Group of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnological Development, Pasteur Institute of Tunis, University of Tunis-El Manar, Tunis, Tunisia
| | - Boutheina Ben Abdelmoumen Mardassi
- Group of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnological Development, Pasteur Institute of Tunis, University of Tunis-El Manar, Tunis, Tunisia
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Zhang N, Julian JD, Zabotina OA. Multiprotein Complexes of Plant Glycosyltransferases Involved in Their Function and Trafficking. PLANTS (BASEL, SWITZERLAND) 2025; 14:350. [PMID: 39942912 PMCID: PMC11820401 DOI: 10.3390/plants14030350] [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: 12/19/2024] [Revised: 01/14/2025] [Accepted: 01/15/2025] [Indexed: 02/16/2025]
Abstract
Plant cells utilize protein oligomerization for their functions in numerous important cellular processes. Protein-protein interactions are necessary to stabilize, optimize, and activate enzymes, as well as localize proteins to specific organelles and membranes. Glycosyltransferases-enzymes that attach sugars to polysaccharides, proteins, lipids, and RNA-across multiple plant biosynthetic processes have been demonstrated to interact with one another. The mechanisms behind these interactions are still unknown, but recent research has highlighted extensive examples of protein-protein interactions, specifically in the plant cell wall hemicellulose and pectin biosynthesis that takes place in the Golgi apparatus. In this review, we will discuss what is known so far about the interactions among Golgi-localized glycosyltransferases that are important for their functioning, trafficking, as well as structural aspects.
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Affiliation(s)
| | | | - Olga A. Zabotina
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (N.Z.); (J.D.J.)
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Wu W, Chen L, Liang R, Huang S, Li X, Huang B, Luo H, Zhang M, Wang X, Zhu H. The role of light in regulating plant growth, development and sugar metabolism: a review. FRONTIERS IN PLANT SCIENCE 2025; 15:1507628. [PMID: 39840366 PMCID: PMC11747448 DOI: 10.3389/fpls.2024.1507628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Accepted: 12/11/2024] [Indexed: 01/23/2025]
Abstract
Light provides the necessary energy for plant photosynthesis, which allows plants to produce organic matter and energy conversion, during plant growth and development. Light provides material energy to plants as the basis for cell division and differentiation, chlorophyll synthesis, tissue growth and stomatal movement, and light intensity, photoperiod, and light quality play important roles in these processes. There are several regulatory mechanisms involved in sugar metabolism in plants, and light, as one of the regulatory factors, affects cell wall composition, starch granules, sucrose synthesis, and vascular bundle formation. Similarly, sugar species and genes are affected in the context of light-regulated sugar metabolism. We searched the available databases and found that there are fewer relevant reviews. Therefore, this paper provides a summary of the effects of light on plant growth and development and sugar metabolism, further elaborates on the mechanisms of light effects on plants, and provides some new insights for a better understanding of how plant growth is regulated under different light conditions.
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Affiliation(s)
- Wenyuan Wu
- Guangxi Zhuang and Yao Ethnic Medicine Key Laboratory, Guangxi University of Chinese Medicine, Nanning, China
| | - Long Chen
- Guangxi Zhuang and Yao Ethnic Medicine Key Laboratory, Guangxi University of Chinese Medicine, Nanning, China
- Nutrition and Bromatology Group, Analytical Chemistry and Food Science, Instituto de Agroecoloxía e Alimentación (IAA) – CITEXVI, Universidade de Vigo, Vigo, Spain
| | - Rentao Liang
- Guangxi Zhuang and Yao Ethnic Medicine Key Laboratory, Guangxi University of Chinese Medicine, Nanning, China
| | - Shiping Huang
- Guangxi Zhuang and Yao Ethnic Medicine Key Laboratory, Guangxi University of Chinese Medicine, Nanning, China
| | - Xiang Li
- Guangxi Zhuang and Yao Ethnic Medicine Key Laboratory, Guangxi University of Chinese Medicine, Nanning, China
| | - Bilei Huang
- Guangxi Zhuang and Yao Ethnic Medicine Key Laboratory, Guangxi University of Chinese Medicine, Nanning, China
| | - Huimin Luo
- Guangxi Zhuang and Yao Ethnic Medicine Key Laboratory, Guangxi University of Chinese Medicine, Nanning, China
| | - Miao Zhang
- Guangxi Zhuang and Yao Ethnic Medicine Key Laboratory, Guangxi University of Chinese Medicine, Nanning, China
| | - Xiaoxun Wang
- Guangxi Zhuang and Yao Ethnic Medicine Key Laboratory, Guangxi University of Chinese Medicine, Nanning, China
| | - Hua Zhu
- Guangxi Zhuang and Yao Ethnic Medicine Key Laboratory, Guangxi University of Chinese Medicine, Nanning, China
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Begcy K, Mondragón-Palomino M, Zhou LZ, Seitz PL, Márton ML, Dresselhaus T. Maize stigmas react differently to self- and cross-pollination and fungal invasion. PLANT PHYSIOLOGY 2024; 196:3071-3090. [PMID: 39371027 PMCID: PMC11638485 DOI: 10.1093/plphys/kiae536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 09/11/2024] [Accepted: 09/15/2024] [Indexed: 10/08/2024]
Abstract
During sexual reproduction in flowering plants, tip-growing pollen tubes travel from the stigma inside the maternal tissues of the pistil toward ovules. In maize (Zea mays L.), the stigma is highly elongated, forming thread-like strands known as silks. Only compatible pollen tubes successfully penetrate and grow through the transmitting tract of the silk to reach the ovules. Like pollen, fungal spores germinate at the surface of silks and generate tube-like structures (hyphae) penetrating silk tissue. To elucidate commonalities and differences between silk responses to these distinctive invading cells, we compared growth behavior of the various invaders as well as the silk transcriptome after self-pollination, cross-pollination, and infection using 2 different fungi. We report that self-pollination triggers mainly senescence genes, whereas incompatible pollen from Tripsacum dactyloides leads to downregulation of rehydration, microtubule, and cell wall-related genes, explaining the slower pollen tube growth and arrest. Invasion by the ascomycete Fusarium graminearum triggers numerous defense responses including the activation of monolignol biosynthesis and NAC as well as WRKY transcription factor genes, whereas responses to the basidiomycete Ustilago maydis are generally much weaker. We present evidence that incompatible pollination and fungal infection trigger transcriptional reprograming of maize silks cell wall. Pathogen invasion also activates the phytoalexin biosynthesis pathway.
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Affiliation(s)
- Kevin Begcy
- Environmental Horticulture Department, University of Florida, Gainesville, FL 32611, USA
| | | | - Liang-Zi Zhou
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg 93040, Germany
| | - Patricia-Lena Seitz
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg 93040, Germany
| | - Mihaela-Luiza Márton
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg 93040, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg 93040, Germany
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Bovet L, Battey J, Lu J, Sierro N, Dewey RE, Goepfert S. Nitrate assimilation pathway is impacted in young tobacco plants overexpressing a constitutively active nitrate reductase or displaying a defective CLCNt2. BMC PLANT BIOLOGY 2024; 24:1132. [PMID: 39592946 PMCID: PMC11600588 DOI: 10.1186/s12870-024-05834-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 11/15/2024] [Indexed: 11/28/2024]
Abstract
BACKGROUND We have previously shown that the expression of a constitutively active nitrate reductase variant and the suppression of CLCNt2 gene function (belonging to the chloride channel (CLC) gene family) in field-grown tobacco reduces tobacco-specific nitrosamines (TSNA) accumulation in cured leaves and cigarette smoke. In both cases, TSNA reductions resulted from a strong diminution of free nitrate in the leaf, as nitrate is a precursor of the TSNA-producing nitrosating agents formed during tobacco curing and smoking. These nitrosating agents modify tobacco alkaloids to produce TSNAs, the most problematic of which are NNN (N-nitrosonornicotine) and NNK (4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone). The expression of a deregulated nitrate reductase enzyme (DNR) that is no longer responsive to light regulation is believed to diminish free nitrate pools by immediately channeling incoming nitrate into the nitrate assimilation pathway. The reduction in nitrate observed when the two tobacco gene copies encoding the vacuolar nitrate transporter CLCNt2 were down-regulated by RNAi-mediated suppression or knocked out using the CRISPR-Cas technology was mechanistically distinct; likely attributable to the inability of the tobacco cell to efficiently sequester nitrate into the vacuole where this metabolite is protected from further assimilation. In this study, we used transcriptomic and metabolomic analyses to compare the nitrate assimilation response in tobacco plants either expressing DNR or lacking CLCNt2 function. RESULTS When grown in a controlled environment, both DNR and CLCNt2-KO (CLCKO) plants exhibited (1) reduced nitrate content in the leaf; (2) increased N-assimilation into the amino acids Gln and Asn; and (3) a similar pattern of differential regulation of several genes controlling stress responses, including water stress, and cell wall metabolism in comparison to wild-type plants. Differences in gene regulation were also observed between DNR and CLCKO plants, including genes encoding nitrite reductase and asparagine synthetase. CONCLUSIONS Our data suggest that even though both DNR and CLCKO plants display common characteristics with respect to nitrate assimilation, cellular responses, water stress, and cell wall remodeling, notable differences in gene regulatory patterns between the two low nitrate plants are also observed. These findings open new avenues in using plants fixing more nitrogen into amino acids for plant improvement or nutrition perspectives.
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Affiliation(s)
- L Bovet
- PMI R&D, Philip Morris Products S.A., Quai-Jeanrenaud 5, Neuchâtel, 2000, Switzerland.
| | - J Battey
- PMI R&D, Philip Morris Products S.A., Quai-Jeanrenaud 5, Neuchâtel, 2000, Switzerland
| | - J Lu
- Department of Crop and Soil Sciences, North Carolina State University, Campus Box 8009, Raleigh, NC, 27695, USA
| | - N Sierro
- PMI R&D, Philip Morris Products S.A., Quai-Jeanrenaud 5, Neuchâtel, 2000, Switzerland
| | - R E Dewey
- Department of Crop and Soil Sciences, North Carolina State University, Campus Box 8009, Raleigh, NC, 27695, USA
| | - S Goepfert
- PMI R&D, Philip Morris Products S.A., Quai-Jeanrenaud 5, Neuchâtel, 2000, Switzerland
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De Coninck T, Desmet T, Van Damme EJM. Carbohydrate-active enzymes involved in rice cell wall metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:6206-6227. [PMID: 38980746 DOI: 10.1093/jxb/erae295] [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: 05/08/2024] [Accepted: 07/04/2024] [Indexed: 07/11/2024]
Abstract
Plant cell walls are complex, multifunctional structures, built up of polysaccharides and proteins. The configuration and abundance of cell wall constituents determine cellular elongation and plant growth. The emphasis of this review is on rice, a staple crop with economic importance, serving as model for grasses/cereals. Recent advancements have contributed to a better understanding of the grass/cereal cell wall. This review brings together current knowledge of the organization and metabolism of the rice cell wall, and addresses gaps in the information regarding the cell wall and enzymes involved. Several cell wall fractions, including cellulose, mixed-linkage glucans, and glucuronoarabinoxylans, are well understood in rice and other grasses/grains. Conversely, there are still open questions and missing links in relation to xyloglucans, glucomannans, pectin, lignin, and arabinogalactan proteins. There is still a large and untapped potential to identify carbohydrate-active enzymes (CAZymes), to characterize their activity, and to elucidate their involvement in the metabolism of the mentioned cell wall fractions. This review highlights the involvement of carbohydrate-active enzymes in rice cell wall metabolism, providing an update of current understanding with the aim of demarcating research areas with potential for further investigations.
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Affiliation(s)
- Tibo De Coninck
- Laboratory for Biochemistry & Glycobiology, Department of Biotechnology, Ghent University, Proeftuinstraat 86, 9000 Ghent, Belgium
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Els J M Van Damme
- Laboratory for Biochemistry & Glycobiology, Department of Biotechnology, Ghent University, Proeftuinstraat 86, 9000 Ghent, Belgium
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Wan Y, Huang J, Tang Q, Zhang S, Qin H, Dong Y, Wang X, Qiu C, Huang M, Zhang Z, Zhang Y, Zhou R. Characterizing the Contribution of Functional Microbiota Cultures in Pit Mud to the Metabolite Profiles of Fermented Grains. Foods 2024; 13:1597. [PMID: 38890826 PMCID: PMC11171501 DOI: 10.3390/foods13111597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/14/2024] [Accepted: 05/19/2024] [Indexed: 06/20/2024] Open
Abstract
Elevating the flavor profile of strong flavors Baijiu has always been a focal point in the industry, and pit mud (PM) serves as a crucial flavor contributor in the fermentation process of the fermented grains (FG). This study investigated the influence of wheat flour and bran (MC and FC) as PM culture enrichment media on the microbiota and metabolites of FG, aiming to inform strategies for improving strong-flavor Baijiu flavor. Results showed that adding PM cultures to FG significantly altered its properties: FC enhanced starch degradation to 51.46% and elevated reducing sugar content to 1.60%, while MC increased acidity to 2.11 mmol/10 g. PM cultures also elevated FG's ester content, with increases of 0.36 times for MC-FG60d and 1.48 times for FC-FG60d compared to controls, and ethyl hexanoate rising by 0.91 times and 1.39 times, respectively. Microbial analysis revealed that Lactobacillus constituted over 95% of the Abundant bacteria community, with Kroppenstedtia or Bacillus being predominant among Rare bacteria. Abundant fungi included Rasamsonia, Pichia, and Thermomyces, while Rare fungi consisted of Rhizopus and Malassezia. Metagenomic analysis revealed bacterial dominance, primarily consisting of Lactobacillus and Acetilactobacillus (98.80-99.40%), with metabolic function predictions highlighting genes related to metabolism, especially in MC-FG60d. Predictions from PICRUSt2 suggested control over starch, cellulose degradation, and the TCA cycle by fungal subgroups, while Abundant fungi and bacteria regulated ethanol and lactic acid production. This study highlights the importance of PM cultures in the fermentation process of FG, which is significant for brewing high-quality, strong-flavor Baijiu.
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Affiliation(s)
- Yingdong Wan
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (Y.W.); (J.H.); (Q.T.); (Z.Z.); (Y.Z.)
| | - Jun Huang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (Y.W.); (J.H.); (Q.T.); (Z.Z.); (Y.Z.)
| | - Qiuxiang Tang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (Y.W.); (J.H.); (Q.T.); (Z.Z.); (Y.Z.)
| | - Suyi Zhang
- Luzhou Lao Jiao Co., Ltd., Luzhou 646699, China; (S.Z.); (H.Q.); (Y.D.); (X.W.); (C.Q.); (M.H.)
| | - Hui Qin
- Luzhou Lao Jiao Co., Ltd., Luzhou 646699, China; (S.Z.); (H.Q.); (Y.D.); (X.W.); (C.Q.); (M.H.)
| | - Yi Dong
- Luzhou Lao Jiao Co., Ltd., Luzhou 646699, China; (S.Z.); (H.Q.); (Y.D.); (X.W.); (C.Q.); (M.H.)
| | - Xiaojun Wang
- Luzhou Lao Jiao Co., Ltd., Luzhou 646699, China; (S.Z.); (H.Q.); (Y.D.); (X.W.); (C.Q.); (M.H.)
| | - Chuanfeng Qiu
- Luzhou Lao Jiao Co., Ltd., Luzhou 646699, China; (S.Z.); (H.Q.); (Y.D.); (X.W.); (C.Q.); (M.H.)
| | - Mengyang Huang
- Luzhou Lao Jiao Co., Ltd., Luzhou 646699, China; (S.Z.); (H.Q.); (Y.D.); (X.W.); (C.Q.); (M.H.)
| | - Zhu Zhang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (Y.W.); (J.H.); (Q.T.); (Z.Z.); (Y.Z.)
| | - Yi Zhang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (Y.W.); (J.H.); (Q.T.); (Z.Z.); (Y.Z.)
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China; (Y.W.); (J.H.); (Q.T.); (Z.Z.); (Y.Z.)
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Delmer D, Dixon RA, Keegstra K, Mohnen D. The plant cell wall-dynamic, strong, and adaptable-is a natural shapeshifter. THE PLANT CELL 2024; 36:1257-1311. [PMID: 38301734 PMCID: PMC11062476 DOI: 10.1093/plcell/koad325] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/19/2023] [Indexed: 02/03/2024]
Abstract
Mythology is replete with good and evil shapeshifters, who, by definition, display great adaptability and assume many different forms-with several even turning themselves into trees. Cell walls certainly fit this definition as they can undergo subtle or dramatic changes in structure, assume many shapes, and perform many functions. In this review, we cover the evolution of knowledge of the structures, biosynthesis, and functions of the 5 major cell wall polymer types that range from deceptively simple to fiendishly complex. Along the way, we recognize some of the colorful historical figures who shaped cell wall research over the past 100 years. The shapeshifter analogy emerges more clearly as we examine the evolving proposals for how cell walls are constructed to allow growth while remaining strong, the complex signaling involved in maintaining cell wall integrity and defense against disease, and the ways cell walls adapt as they progress from birth, through growth to maturation, and in the end, often function long after cell death. We predict the next century of progress will include deciphering cell type-specific wall polymers; regulation at all levels of polymer production, crosslinks, and architecture; and how walls respond to developmental and environmental signals to drive plant success in diverse environments.
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Affiliation(s)
- Deborah Delmer
- Section of Plant Biology, University of California Davis, Davis, CA 95616, USA
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Kenneth Keegstra
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48823, USA
| | - Debra Mohnen
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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Lathe RS, McFarlane HE, Kesten C, Wang L, Khan GA, Ebert B, Ramírez-Rodríguez EA, Zheng S, Noord N, Frandsen K, Bhalerao RP, Persson S. NKS1/ELMO4 is an integral protein of a pectin synthesis protein complex and maintains Golgi morphology and cell adhesion in Arabidopsis. Proc Natl Acad Sci U S A 2024; 121:e2321759121. [PMID: 38579009 PMCID: PMC11009649 DOI: 10.1073/pnas.2321759121] [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: 01/03/2024] [Accepted: 03/07/2024] [Indexed: 04/07/2024] Open
Abstract
Adjacent plant cells are connected by specialized cell wall regions, called middle lamellae, which influence critical agricultural characteristics, including fruit ripening and organ abscission. Middle lamellae are enriched in pectin polysaccharides, specifically homogalacturonan (HG). Here, we identify a plant-specific Arabidopsis DUF1068 protein, called NKS1/ELMO4, that is required for middle lamellae integrity and cell adhesion. NKS1 localizes to the Golgi apparatus and loss of NKS1 results in changes to Golgi structure and function. The nks1 mutants also display HG deficient phenotypes, including reduced seedling growth, changes to cell wall composition, and tissue integrity defects. These phenotypes are comparable to qua1 and qua2 mutants, which are defective in HG biosynthesis. Notably, genetic interactions indicate that NKS1 and the QUAs work in a common pathway. Protein interaction analyses and modeling corroborate that they work together in a stable protein complex with other pectin-related proteins. We propose that NKS1 is an integral part of a large pectin synthesis protein complex and that proper function of this complex is important to support Golgi structure and function.
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Affiliation(s)
- Rahul S. Lathe
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
- Max-Planck Institute for Molecular Plant Physiology, Potsdam14476, Germany
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, UmeåSE-90187, Sweden
| | - Heather E. McFarlane
- Department of Cell & Systems Biology, University of Toronto, Toronto, ONM5S 3G5, Canada
- School of Biosciences, University of Melbourne, Parkville, VIC3010, Australia
| | - Christopher Kesten
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
| | - Liu Wang
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
- School of Biosciences, University of Melbourne, Parkville, VIC3010, Australia
| | - Ghazanfar Abbas Khan
- School of Biosciences, University of Melbourne, Parkville, VIC3010, Australia
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC3086, Australia
| | - Berit Ebert
- School of Biosciences, University of Melbourne, Parkville, VIC3010, Australia
- Department of Biology and Biotechnology, Ruhr University Bochum, Bochum44780, Germany
| | | | - Shuai Zheng
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
| | - Niels Noord
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, UmeåSE-90187, Sweden
| | - Kristian Frandsen
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
| | - Rishikesh P. Bhalerao
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, UmeåSE-90187, Sweden
| | - Staffan Persson
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
- Max-Planck Institute for Molecular Plant Physiology, Potsdam14476, Germany
- School of Biosciences, University of Melbourne, Parkville, VIC3010, Australia
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, University of AdelaideJoint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
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10
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Xu M, Hu J, Li H, Li K, Xu D. Research overview on the genetic mechanism underlying the biosynthesis of polysaccharide in tuber plants. PeerJ 2024; 12:e17052. [PMID: 38464751 PMCID: PMC10924778 DOI: 10.7717/peerj.17052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/13/2024] [Indexed: 03/12/2024] Open
Abstract
Tuber plants are of great significance in the world as human food crops. Polysaccharides, important metabolites in tuber plants, also serve as a source of innovative drugs with significant pharmacological effects. These drugs are particularly known for their immunomodulation and antitumor properties. To fully exploit the potential value of tuber plant polysaccharides and establish a synthetic system for their targeted synthesis, it is crucial to dissect their metabolic processes and genetic regulatory mechanisms. In this article, we provide a comprehensive summary of the basic pathways involved in the synthesis of various types of tuber plant polysaccharides. We also outline the key research progress that has been made in this area in recent years. We classify the main types and functions of tuber plant polysaccharides and analyze the biosynthetic processes and genetic regulation mechanisms of key enzymes involved in the metabolic pathways of starch, cellulose, pectin, and fructan in tuber plants. We have identified hexokinase and glycosyltransferase as the key enzymes involved in the polysaccharide synthesis process. By elucidating the synthesis pathway of polysaccharides in tuber plants and understanding the underlying mechanism of action of key enzymes in the metabolic pathway, we can provide a theoretical framework for enhancing the yield of polysaccharides and other metabolites in plant culture cells. This will ultimately lead to increased production efficiency.
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Affiliation(s)
- Mengwei Xu
- Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jiao Hu
- Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi, Guizhou, China
| | - Hongwei Li
- Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi, Guizhou, China
| | - Kunqian Li
- Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi, Guizhou, China
| | - Delin Xu
- Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi, Guizhou, China
- Guizhou Provincial Demonstration Center of Basic Medical Experimental Teaching, Zunyi Medical University, Zunyi, Guizhou, China
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Li J, Wang BX, Zhang J, Han N, Liu ST, Geng WJ, Jia SR, Li YR, Gan Q, Han PP. A newly discovered glycosyltransferase gene UGT88A1 affects growth and polysaccharide synthesis of Grifola frondosa. Appl Microbiol Biotechnol 2024; 108:246. [PMID: 38421403 PMCID: PMC10904514 DOI: 10.1007/s00253-024-13062-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 03/02/2024]
Abstract
Grifola frodosa polysaccharides, especially β-D-glucans, possess significant anti-tumor, antioxidant and immunostimulatory activities. However, the synthesis mechanism remains to be elucidated. A newly discovered glycosyltransferase UGT88A1 was found to extend glucan chains in vitro. However, the role of UGT88A1 in the growth and polysaccharide synthesis of G. frondosa in vivo remains unclear. In this study, the overexpression of UGT88A1 improved mycelial growth, increased polysaccharide production, and decreased cell wall pressure sensitivity. Biomass and polysaccharide production decreased in the silenced strain, and the pressure sensitivity of the cell wall increased. Overexpression and silencing of UGT88A1 both affected the monosaccharide composition and surface morphology of G. frondosa polysaccharides and influenced the antioxidant activity of polysaccharides from different strains. The messenger RNA expression of glucan synthase (GLS), UTP-glucose-1-phosphate uridylyltransferase (UGP), and UDP-xylose-4-epimerase (UXE) related to polysaccharide synthesis, and genes related to cell wall integrity increased in the overexpression strain. Overall, our study indicates that UGT88A1 plays an important role in the growth, stress, and polysaccharide synthesis of G. frondosa, providing a reference for exploring the pathway of polysaccharide synthesis and metabolic regulation. KEY POINTS: •UGT88A1 plays an important role in the growth, stress response, and polysaccharide synthesis in G. frondosa. •UGT88A1 affected the monosaccharide composition, surface morphology and antioxidant activity of G. frondosa polysaccharides. •UGT88A1 regulated the mRNA expression of genes related to polysaccharide synthesis and cell wall integrity.
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Affiliation(s)
- Jian Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Bao-Xin Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Jie Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Na Han
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Shu-Ting Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Wen-Ji Geng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Shi-Ru Jia
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Yan-Ru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Quan Gan
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Pei-Pei Han
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
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12
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Taliei F, Sabouri H, Kazerani B, Ghasemi S. Finding stable and closely linked QTLs against spot blotch in different planting dates during the adult stage in barley. Sci Rep 2024; 14:818. [PMID: 38191625 PMCID: PMC10774436 DOI: 10.1038/s41598-024-51358-3] [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: 07/14/2023] [Accepted: 01/03/2024] [Indexed: 01/10/2024] Open
Abstract
The common resistance to Spot Blotch (SB) and drought stress in barley was studied using a RILs population caused Kavir × Badia cross. These lines were inoculated with Cochliobolus sativus Gonbad isolate during the adult stage and were evaluated for three crop seasons in different planting dates. The different osmotic potentials during the flowering were regulated by changing the planting dates. In total, 43 lines had resistant to SB and drought. The high-density linkage map covered 1045 cM of barley genome. A total of five stable and closely linked QTLs to SB resistance were mapped on chromosomes 2H, 3H, 4H and 7H using genome-wide composite interval mapping. Moreover, four stable and closely linked QTLs to SB susceptibility were located on chromosomes 3H, 4H, 5H and 7H. Additionally, the ISJ19-A, SCoT7-C, ISJ17-B, Bmac0144k, iPBS2415-1, Bmac0282b and EBmatc0016 markers can be used for positive screening of resistant cultivars. However, ISJ3-C, UMB310, ISJ9-B, UMB706, D03-D and iPBS2257-A markers can be used for negative screening of susceptible cultivars in marker-assisted selection. The bioinformatics studies showed that QRCsa-2H (ISJ19-A region), QRCsa-2H (SCoT7-C-ISJ17-B region), QRCsa-3H (Bmac0144k region), QRCsa-4H (iPBS2415-1 region) and QRCsa-7H (Bmac0282b-EBmatc0016 region) are involved in the carboxypeptidase, Glycosyltransferase, transcription factors, kinase and AP2/ERF, respectively.
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Affiliation(s)
- Fakhtak Taliei
- Department of Plant Production, College of Agriculture Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous, Iran.
| | - Hossein Sabouri
- Department of Plant Production, College of Agriculture Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous, Iran
| | - Borzo Kazerani
- Department of Plant Breeding and Biotechnology, Faculty of Plant Production, Gorgan University of Agricultural Science and Natural Resources, Gorgan, Iran
| | - Shahram Ghasemi
- Department of Plant Production, College of Agriculture Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous, Iran
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Al-Khayri JM, Rashmi R, Toppo V, Chole PB, Banadka A, Sudheer WN, Nagella P, Shehata WF, Al-Mssallem MQ, Alessa FM, Almaghasla MI, Rezk AAS. Plant Secondary Metabolites: The Weapons for Biotic Stress Management. Metabolites 2023; 13:716. [PMID: 37367873 DOI: 10.3390/metabo13060716] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
The rise in global temperature also favors the multiplication of pests and pathogens, which calls into question global food security. Plants have developed special coping mechanisms since they are sessile and lack an immune system. These mechanisms use a variety of secondary metabolites as weapons to avoid obstacles, adapt to their changing environment, and survive in less-than-ideal circumstances. Plant secondary metabolites include phenolic compounds, alkaloids, glycosides, and terpenoids, which are stored in specialized structures such as latex, trichomes, resin ducts, etc. Secondary metabolites help the plants to be safe from biotic stressors, either by repelling them or attracting their enemies, or exerting toxic effects on them. Modern omics technologies enable the elucidation of the structural and functional properties of these metabolites along with their biosynthesis. A better understanding of the enzymatic regulations and molecular mechanisms aids in the exploitation of secondary metabolites in modern pest management approaches such as biopesticides and integrated pest management. The current review provides an overview of the major plant secondary metabolites that play significant roles in enhancing biotic stress tolerance. It examines their involvement in both indirect and direct defense mechanisms, as well as their storage within plant tissues. Additionally, this review explores the importance of metabolomics approaches in elucidating the significance of secondary metabolites in biotic stress tolerance. The application of metabolic engineering in breeding for biotic stress resistance is discussed, along with the exploitation of secondary metabolites for sustainable pest management.
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Affiliation(s)
- Jameel M Al-Khayri
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Ramakrishnan Rashmi
- Department of Life Sciences, CHRIST (Deemed to be University), Bangalore 560 029, Karnataka, India
| | - Varsha Toppo
- Department of Life Sciences, CHRIST (Deemed to be University), Bangalore 560 029, Karnataka, India
| | - Pranjali Bajrang Chole
- Department of Life Sciences, CHRIST (Deemed to be University), Bangalore 560 029, Karnataka, India
| | - Akshatha Banadka
- Department of Life Sciences, CHRIST (Deemed to be University), Bangalore 560 029, Karnataka, India
| | - Wudali Narasimha Sudheer
- Department of Life Sciences, CHRIST (Deemed to be University), Bangalore 560 029, Karnataka, India
| | - Praveen Nagella
- Department of Life Sciences, CHRIST (Deemed to be University), Bangalore 560 029, Karnataka, India
| | - Wael Fathi Shehata
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Muneera Qassim Al-Mssallem
- Department of Food Science and Nutrition, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Fatima Mohammed Alessa
- Department of Food Science and Nutrition, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Mustafa Ibrahim Almaghasla
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
- Plant Pests, and Diseases Unit, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Adel Abdel-Sabour Rezk
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
- Department of Virus and Phytoplasma, Plant Pathology Institute, Agricultural Research Center, Giza 12619, Egypt
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14
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McFarlane HE. Open questions in plant cell wall synthesis. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad110. [PMID: 36961357 DOI: 10.1093/jxb/erad110] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Indexed: 06/18/2023]
Abstract
Plant cells are surrounded by strong yet flexible polysaccharide-based cell walls that support the cell while also allowing growth by cell expansion. Plant cell wall research has advanced tremendously in recent years. Sequenced genomes of many model and crop plants have facilitated cataloging and characterization of many enzymes involved in cell wall synthesis. Structural information has been generated for several important cell wall synthesizing enzymes. Important tools have been developed including antibodies raised against a variety of cell wall polysaccharides and glycoproteins, collections of enzyme clones and synthetic glycan arrays for characterizing enzymes, herbicides that specifically affect cell wall synthesis, live-cell imaging probes to track cell wall synthesis, and an inducible secondary cell wall synthesis system. Despite these advances, and often because of the new information they provide, many open questions about plant cell wall polysaccharide synthesis persist. This article highlights some of the key questions that remain open, reviews the data supporting different hypotheses that address these questions, and discusses technological developments that may answer these questions in the future.
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Affiliation(s)
- Heather E McFarlane
- Department of Cell & Systems Biology, University of Toronto, 25 Harbord St., Toronto, ON, M5S 3G5, Canada
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15
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Prabhakar PK, Pereira JH, Taujale R, Shao W, Bharadwaj VS, Chapla D, Yang JY, Bomble YJ, Moremen KW, Kannan N, Hammel M, Adams PD, Scheller HV, Urbanowicz BR. Structural and biochemical insight into a modular β-1,4-galactan synthase in plants. NATURE PLANTS 2023; 9:486-500. [PMID: 36849618 PMCID: PMC10115243 DOI: 10.1038/s41477-023-01358-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/25/2023] [Indexed: 05/18/2023]
Abstract
Rhamnogalacturonan I (RGI) is a structurally complex pectic polysaccharide with a backbone of alternating rhamnose and galacturonic acid residues substituted with arabinan and galactan side chains. Galactan synthase 1 (GalS1) transfers galactose and arabinose to either extend or cap the β-1,4-galactan side chains of RGI, respectively. Here we report the structure of GalS1 from Populus trichocarpa, showing a modular protein consisting of an N-terminal domain that represents the founding member of a new family of carbohydrate-binding module, CBM95, and a C-terminal glycosyltransferase family 92 (GT92) catalytic domain that adopts a GT-A fold. GalS1 exists as a dimer in vitro, with stem domains interacting across the chains in a 'handshake' orientation that is essential for maintaining stability and activity. In addition to understanding the enzymatic mechanism of GalS1, we gained insight into the donor and acceptor substrate binding sites using deep evolutionary analysis, molecular simulations and biochemical studies. Combining all the results, a mechanism for GalS1 catalysis and a new model for pectic galactan side-chain addition are proposed.
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Affiliation(s)
- Pradeep Kumar Prabhakar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, USA
| | - Jose Henrique Pereira
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rahil Taujale
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Wanchen Shao
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vivek S Bharadwaj
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Natarajan Kannan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Breeanna R Urbanowicz
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, USA.
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Esuma W, Eyoo O, Gwandu F, Mukasa S, Alicai T, Ozimati A, Nuwamanya E, Rabbi I, Kawuki R. Validation of KASP markers associated with cassava mosaic disease resistance, storage root dry matter and provitamin A carotenoid contents in Ugandan cassava germplasm. FRONTIERS IN PLANT SCIENCE 2022; 13:1017275. [PMID: 36507387 PMCID: PMC9727383 DOI: 10.3389/fpls.2022.1017275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION The intrinsic high heterozygosity of cassava makes conventional breeding ineffective for rapid genetic improvement. However, recent advances in next generation sequencing technologies have enabled the use of high-density markers for genome-wide association studies, aimed at identifying single nucleotide polymorphisms (SNPs) linked to major traits such as cassava mosaic disease (CMD) resistance, dry matter content (DMC) and total carotenoids content (TCC). A number of these trait-linked SNPs have been converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers for downstream application of marker assisted selection. METHODS We assayed 13 KASP markers to evaluate their effectiveness in selecting for CMD, DMC and TCC in 1,677 diverse cassava genotypes representing two independent breeding populations in Uganda. RESULTS Five KASP markers had significant co-segregation with phenotypes; CMD resistance (2), DMC (1) and TCC (2), with each marker accounting for at least 30% of the phenotypic variation. Markers located within the chromosomal regions for which strong marker-trait association loci have been characterised (chromosome 12 markers for CMD, chromosome 1 markers for DMC and TCC) had consistently superior ability to discriminate the respective phenotypes. DISCUSSION The results indicate varying discriminatory abilities of the KASP markers assayed and the need for their context-based use for MAS, with PSY2_572 particularly effective in selecting for high TCC. Availing the effective KASP markers on cost-effective genotyping platforms could facilitate practical implementation of marker-assisted cassava breeding for accelerated genetic gains for CMD, DMC and provitamin A carotenoids.
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Affiliation(s)
- Williams Esuma
- National Crops Resources Research Institute, Kampala, Uganda
| | - Oscar Eyoo
- National Crops Resources Research Institute, Kampala, Uganda
- College of Natural Sciences, Department of Plant Sciences, Microbiology and Biotechnology, Makerere University, Kampala, Uganda
| | - Francisca Gwandu
- College of Natural Sciences, Department of Plant Sciences, Microbiology and Biotechnology, Makerere University, Kampala, Uganda
| | - Settumba Mukasa
- College of Natural Sciences, Department of Plant Sciences, Microbiology and Biotechnology, Makerere University, Kampala, Uganda
| | - Titus Alicai
- National Crops Resources Research Institute, Kampala, Uganda
| | - Alfred Ozimati
- National Crops Resources Research Institute, Kampala, Uganda
- College of Natural Sciences, Department of Plant Sciences, Microbiology and Biotechnology, Makerere University, Kampala, Uganda
| | | | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), Oyo, Nigeria
| | - Robert Kawuki
- National Crops Resources Research Institute, Kampala, Uganda
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17
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Pfeifer L, Mueller KK, Classen B. The cell wall of hornworts and liverworts: innovations in early land plant evolution? JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4454-4472. [PMID: 35470398 DOI: 10.1093/jxb/erac157] [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: 12/07/2021] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
An important step for plant diversification was the transition from freshwater to terrestrial habitats. The bryophytes and all vascular plants share a common ancestor that was probably the first to adapt to life on land. A polysaccharide-rich cell wall was necessary to cope with newly faced environmental conditions. Therefore, some pre-requisites for terrestrial life have to be shared in the lineages of modern bryophytes and vascular plants. This review focuses on hornwort and liverwort cell walls and aims to provide an overview on shared and divergent polysaccharide features between these two groups of bryophytes and vascular plants. Analytical, immunocytochemical, and bioinformatic data were analysed. The major classes of polysaccharides-cellulose, hemicelluloses, and pectins-seem to be present but have diversified structurally during evolution. Some polysaccharide groups show structural characteristics which separate hornworts from the other bryophytes or are too poorly studied in detail to be able to draw absolute conclusions. Hydroxyproline-rich glycoprotein backbones are found in hornworts and liverworts, and show differences in, for example, the occurrence of glycosylphosphatidylinositol (GPI)-anchored arabinogalactan-proteins, while glycosylation is practically unstudied. Overall, the data are an appeal to researchers in the field to gain more knowledge on cell wall structures in order to understand the changes with regard to bryophyte evolution.
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Affiliation(s)
- Lukas Pfeifer
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, D-24118 Kiel, Germany
| | - Kim-Kristine Mueller
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, D-24118 Kiel, Germany
| | - Birgit Classen
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, D-24118 Kiel, Germany
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18
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Sinclair R, Hsu G, Davis D, Chang M, Rosquete M, Iwasa JH, Drakakaki G. Plant cytokinesis and the construction of new cell wall. FEBS Lett 2022; 596:2243-2255. [PMID: 35695093 DOI: 10.1002/1873-3468.14426] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/10/2022]
Abstract
Cytokinesis in plants is fundamentally different from that in animals and fungi. In plant cells, a cell plate forms through the fusion of cytokinetic vesicles and then develops into the new cell wall, partitioning the cytoplasm of the dividing cell. The formation of the cell plate entails multiple stages that involve highly orchestrated vesicle accumulation, fusion, and membrane maturation, which occur concurrently with the timely deposition of polysaccharides such as callose, cellulose, and cross-linking glycans. This review summarizes the major stages in cytokinesis, endomembrane components involved in cell plate assembly and its transition to a new cell wall. An animation that can be widely used for educational purposes further summarizes the process.
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Affiliation(s)
- Rosalie Sinclair
- Department of Plant Sciences University of California Davis, Davis, CA, 95616, USA
| | - Grace Hsu
- Department of Biochemistry University of Utah, School of Medicine, Salt Lake City, UT, 84112, USA
| | - Destiny Davis
- Department of Plant Sciences University of California Davis, Davis, CA, 95616, USA.,Current address: Lawrence Berkeley National Lab, Emeryville, CA, 94608, USA
| | - Mingqin Chang
- Department of Plant Sciences University of California Davis, Davis, CA, 95616, USA
| | - Michel Rosquete
- Department of Plant Sciences University of California Davis, Davis, CA, 95616, USA.,Current address: Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Janet H Iwasa
- Department of Biochemistry University of Utah, School of Medicine, Salt Lake City, UT, 84112, USA
| | - Georgia Drakakaki
- Department of Plant Sciences University of California Davis, Davis, CA, 95616, USA
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Genome-wide association study identifies loci and candidate genes for grain micronutrients and quality traits in wheat (Triticum aestivum L.). Sci Rep 2022; 12:7037. [PMID: 35487909 PMCID: PMC9054743 DOI: 10.1038/s41598-022-10618-w] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/08/2022] [Indexed: 11/09/2022] Open
Abstract
Malnutrition due to micronutrients and protein deficiency is recognized among the major global health issues. Genetic biofortification of wheat is a cost-effective and sustainable strategy to mitigate the global micronutrient and protein malnutrition. Genomic regions governing grain zinc concentration (GZnC), grain iron concentration (GFeC), grain protein content (GPC), test weight (TW), and thousand kernel weight (TKW) were investigated in a set of 184 diverse bread wheat genotypes through genome-wide association study (GWAS). The GWAS panel was genotyped using Breeders' 35 K Axiom Array and phenotyped in three different environments during 2019-2020. A total of 55 marker-trait associations (MTAs) were identified representing all three sub-genomes of wheat. The highest number of MTAs were identified for GPC (23), followed by TKW (15), TW (11), GFeC (4), and GZnC (2). Further, a stable SNP was identified for TKW, and also pleiotropic regions were identified for GPC and TKW. In silico analysis revealed important putative candidate genes underlying the identified genomic regions such as F-box-like domain superfamily, Zinc finger CCCH-type proteins, Serine-threonine/tyrosine-protein kinase, Histone deacetylase domain superfamily, and SANT/Myb domain superfamily proteins, etc. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection.
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Zhang N, Zabotina OA. Critical Determinants in ER-Golgi Trafficking of Enzymes Involved in Glycosylation. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030428. [PMID: 35161411 PMCID: PMC8840164 DOI: 10.3390/plants11030428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 05/03/2023]
Abstract
All living cells generate structurally complex and compositionally diverse spectra of glycans and glycoconjugates, critical for organismal evolution, development, functioning, defense, and survival. Glycosyltransferases (GTs) catalyze the glycosylation reaction between activated sugar and acceptor substrate to synthesize a wide variety of glycans. GTs are distributed among more than 130 gene families and are involved in metabolic processes, signal pathways, cell wall polysaccharide biosynthesis, cell development, and growth. Glycosylation mainly takes place in the endoplasmic reticulum (ER) and Golgi, where GTs and glycosidases involved in this process are distributed to different locations of these compartments and sequentially add or cleave various sugars to synthesize the final products of glycosylation. Therefore, delivery of these enzymes to the proper locations, the glycosylation sites, in the cell is essential and involves numerous secretory pathway components. This review presents the current state of knowledge about the mechanisms of protein trafficking between ER and Golgi. It describes what is known about the primary components of protein sorting machinery and trafficking, which are recognition sites on the proteins that are important for their interaction with the critical components of this machinery.
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Julian JD, Zabotina OA. Xyloglucan Biosynthesis: From Genes to Proteins and Their Functions. FRONTIERS IN PLANT SCIENCE 2022; 13:920494. [PMID: 35720558 PMCID: PMC9201394 DOI: 10.3389/fpls.2022.920494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/13/2022] [Indexed: 05/12/2023]
Abstract
The plant's recalcitrant cell wall is composed of numerous polysaccharides, including cellulose, hemicellulose, and pectin. The most abundant hemicellulose in dicot cell walls is xyloglucan, which consists of a β-(1- > 4) glucan backbone with α-(1- > 6) xylosylation producing an XXGG or XXXG pattern. Xylose residues of xyloglucan are branched further with different patterns of arabinose, fucose, galactose, and acetylation that varies between species. Although xyloglucan research in other species lag behind Arabidopsis thaliana, significant advances have been made into the agriculturally relevant species Oryza sativa and Solanum lycopersicum, which can be considered model organisms for XXGG type xyloglucan. In this review, we will present what is currently known about xyloglucan biosynthesis in A. thaliana, O. sativa, and S. lycopersicum and discuss the recent advances in the characterization of the glycosyltransferases involved in this complex process and their organization in the Golgi.
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Affiliation(s)
- Jordan D Julian
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Olga A Zabotina
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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De Coninck T, Gistelinck K, Janse van Rensburg HC, Van den Ende W, Van Damme EJM. Sweet Modifications Modulate Plant Development. Biomolecules 2021; 11:756. [PMID: 34070047 PMCID: PMC8158104 DOI: 10.3390/biom11050756] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/28/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023] Open
Abstract
Plant development represents a continuous process in which the plant undergoes morphological, (epi)genetic and metabolic changes. Starting from pollination, seed maturation and germination, the plant continues to grow and develops specialized organs to survive, thrive and generate offspring. The development of plants and the interplay with its environment are highly linked to glycosylation of proteins and lipids as well as metabolism and signaling of sugars. Although the involvement of these protein modifications and sugars is well-studied, there is still a long road ahead to profoundly comprehend their nature, significance, importance for plant development and the interplay with stress responses. This review, approached from the plants' perspective, aims to focus on some key findings highlighting the importance of glycosylation and sugar signaling for plant development.
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Affiliation(s)
- Tibo De Coninck
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
| | - Koen Gistelinck
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
| | - Henry C. Janse van Rensburg
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; (H.C.J.v.R.); (W.V.d.E.)
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; (H.C.J.v.R.); (W.V.d.E.)
| | - Els J. M. Van Damme
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
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