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Chalivendra S, Shi S, Li X, Kuang Z, Giovinazzo J, Zhang L, Rossi J, Wang J, Saviola A, Welty R, Liu S, Vaeth K, Zhou ZH, Hansen K, Taliaferro JM, Zhao R. Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast. RNA 2024:rna.079917.123. [PMID: 38688558 DOI: 10.1261/rna.079917.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
The recognition of 5' splice site (5' ss) is one of the earliest steps of pre-mRNA splicing. To better understand the mechanism and regulation of 5' ss recognition, we selectively humanized components of the yeast U1 snRNP to reveal the function of these components in 5' ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yeast U1 (yU1) snRNA and the 5' ss RNA duplex. We replaced the Zinc-Finger (ZnF) domain of yU1C with its human counterpart, which resulted in a cold-sensitive growth phenotype and moderate splicing defects. We next added an auxin-inducible degron to yLuc7 protein (to mimic the lack of Luc7Ls in human U1 snRNP) and found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of PRP40 and Snu71 (two other essential yeast U1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7-Prp40-Snu71 trimer into yeast U1 snRNP, and splicing plays a major role in the regulation of mitochondrial function in yeast.
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Affiliation(s)
- Subbaiah Chalivendra
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics
| | - Shasha Shi
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics
| | - Xueni Li
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics
| | - Zhiling Kuang
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics
| | - Joseph Giovinazzo
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics
| | - Lingdi Zhang
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics
| | - John Rossi
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics
| | - Jingxin Wang
- University of Kansas, Lawrence, Department of Medicinal Chemistry
| | - Anthony Saviola
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics
| | - Robb Welty
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics
| | - Shiheng Liu
- University of California, Los Angeles, CA, Department of Microbiology, Immunology, and Molecular Genetics
| | - Katherine Vaeth
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics
| | - Z Hong Zhou
- University of California, Los Angeles, CA, Department of Microbiology, Immunology, and Molecular Genetics
| | - Kirk Hansen
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics
| | - J Matthew Taliaferro
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics
| | - Rui Zhao
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics;
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Chalivendra S, Shi S, Li X, Kuang Z, Giovinazzo J, Zhang L, Rossi J, Saviola AJ, Wang J, Welty R, Liu S, Vaeth K, Zhou ZH, Hansen KC, Taliaferro JM, Zhao R. Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast. bioRxiv 2023:2023.12.15.571893. [PMID: 38168357 PMCID: PMC10760170 DOI: 10.1101/2023.12.15.571893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The recognition of 5' splice site (5' ss) is one of the earliest steps of pre-mRNA splicing. To better understand the mechanism and regulation of 5' ss recognition, we selectively humanized components of the yeast U1 snRNP to reveal the function of these components in 5' ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yeast U1 (yU1) snRNA and the 5' ss RNA duplex. We replaced the Zinc-Finger (ZnF) domain of yU1C with its human counterpart, which resulted in cold-sensitive growth phenotype and moderate splicing defects. Next, we added an auxin-inducible degron to yLuc7 protein and found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of PRP40 and Snu71 (two other essential yeast U1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe 2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7-Prp40-Snu71 trimer into yeast U1 snRNP, and splicing plays a major role in the regulation of mitochondria function in yeast.
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Moore GG, Chalivendra S, Mack BM, Gilbert MK, Cary JW, Rajasekaran K. Microbiota of maize kernels as influenced by Aspergillus flavus infection in susceptible and resistant inbreds. Front Microbiol 2023; 14:1291284. [PMID: 38029119 PMCID: PMC10657875 DOI: 10.3389/fmicb.2023.1291284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Background Nearly everything on Earth harbors a microbiome. A microbiome is a community of microbes (bacteria, fungi, and viruses) with potential to form complex networks that involve mutualistic and antagonistic interactions. Resident microbiota on/in an organism are determined by the external environment, both biotic and abiotic, and the intrinsic adaptability of each organism. Although the maize microbiome has been characterized, community changes that result from the application of fungal biocontrol strains, such as non-aflatoxigenic Aspergillus flavus, have not. Methods We silk channel inoculated field-grown maize separately with a non-aflatoxigenic biocontrol strain (K49), a highly toxigenic strain (Tox4), and a combination of both A. flavus strains. Two maize inbreds were treated, A. flavus-susceptible B73 and A. flavus-resistant CML322. We then assessed the impacts of A. flavus introduction on the epibiota and endobiota of their maize kernels. Results We found that the native microbial communities were significantly affected, irrespective of genotype or sampled tissue. Overall, bacteriomes exhibited greater diversity of genera than mycobiomes. The abundance of certain genera was unchanged by treatment, including genera of bacteria (e.g., Enterobacter, Pantoea) and fungi (e.g., Sarocladium, Meyerozyma) that are known to be beneficial, antagonistic, or both on plant growth and health. Conclusion Beneficial microbes like Sarocladium that responded well to A. flavus biocontrol strains are expected to enhance biocontrol efficacy, while also displacing/antagonizing harmful microbes.
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Affiliation(s)
- Geromy G. Moore
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, United States
| | - Subbaiah Chalivendra
- Department of Plant Pathology and Crop Physiology, College of Agriculture, Louisiana State University, Baton Rouge, LA, United States
| | - Brian M. Mack
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, United States
| | - Matthew K. Gilbert
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, United States
| | - Jeffrey W. Cary
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, United States
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Abstract
Invertebrate pests, such as insects and nematodes, not only cause or transmit human and livestock diseases but also impose serious crop losses by direct injury as well as vectoring pathogenic microbes. The damage is global but greater in developing countries, where human health and food security are more at risk. Although synthetic pesticides have been in use, biological control measures offer advantages via their biodegradability, environmental safety and precise targeting. This is amply demonstrated by the successful and widespread use of Bacillusthuringiensis to control mosquitos and many plant pests, the latter by the transgenic expression of insecticidal proteins from B. thuringiensis in crop plants. Here, I discuss the prospects of using bacterial and fungal toxins for pest control, including the molecular basis of their biocidal activity.
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Pantha P, Chalivendra S, Oh DH, Elderd BD, Dassanayake M. A Tale of Two Transcriptomic Responses in Agricultural Pests via Host Defenses and Viral Replication. Int J Mol Sci 2021; 22:3568. [PMID: 33808210 PMCID: PMC8037200 DOI: 10.3390/ijms22073568] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 01/02/2023] Open
Abstract
Autographa californica Multiple Nucleopolyhedrovirus (AcMNPV) is a baculovirus that causes systemic infections in many arthropod pests. The specific molecular processes underlying the biocidal activity of AcMNPV on its insect hosts are largely unknown. We describe the transcriptional responses in two major pests, Spodoptera frugiperda (fall armyworm) and Trichoplusia ni (cabbage looper), to determine the host-pathogen responses during systemic infection, concurrently with the viral response to the host. We assembled species-specific transcriptomes of the hemolymph to identify host transcriptional responses during systemic infection and assessed the viral transcript abundance in infected hemolymph from both species. We found transcriptional suppression of chitin metabolism and tracheal development in infected hosts. Synergistic transcriptional support was observed to suggest suppression of immune responses and induction of oxidative stress indicating disease progression in the host. The entire AcMNPV core genome was expressed in the infected host hemolymph with a proportional high abundance detected for viral transcripts associated with replication, structure, and movement. Interestingly, several of the host genes that were targeted by AcMNPV as revealed by our study are also targets of chemical insecticides currently used commercially to control arthropod pests. Our results reveal an extensive overlap between biological processes represented by transcriptional responses in both hosts, as well as convergence on highly abundant viral genes expressed in the two hosts, providing an overview of the host-pathogen transcriptomic landscape during systemic infection.
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Affiliation(s)
| | | | | | - Bret D. Elderd
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (P.P.); (S.C.); (D.-H.O.)
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (P.P.); (S.C.); (D.-H.O.)
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Chalivendra S, Huang F, Busman M, Williams WP, Ham JH. Low Aflatoxin Levels in Aspergillus flavus-Resistant Maize Are Correlated With Increased Corn Earworm Damage and Enhanced Seed Fumonisin. Front Plant Sci 2020; 11:565323. [PMID: 33101334 PMCID: PMC7546873 DOI: 10.3389/fpls.2020.565323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Preharvest mycotoxin contamination of field-grown crops is influenced not only by the host genotype, but also by inoculum load, insect pressure and their confounding interactions with seasonal weather. In two different field trials, we observed a preference in the natural infestation of corn earworm (CEW; Helicoverpa zea Boddie) to specific maize (Zea mays L.) genotypes and investigated this observation. The field trials involved four maize lines with contrasting levels of resistance to Aspergillus flavus. The resistant lines had 7 to 14-fold greater infested ears than the susceptible lines. Seed aflatoxin B1 (AF) levels, in mock- and A. flavus-inoculated ears were consistent with genotype resistance to A. flavus, in that the resistant lines showed low levels of AF (<30 ppb), whereas the susceptible lines had up to 500 ppb. On the other hand, CEW infestation showed a positive correlation with seed fumonisins (FUM) contamination by native Fusarium verticillioides strains. We inferred that the inverse trend in the correlation of AF and FUM with H. zea infestation may be due to a differential sensitivity of CEW to the two mycotoxins. This hypothesis was tested by toxin-feeding studies. H. zea larvae showed decreasing mass with increasing AF in the diet and incurred >30% lethality at 250 ppb. In contrast, CEW was tolerant to fumonisin with no significant loss in larval mass even at 100 ppm, implicating the low seed aflatoxin content as a predominant factor for the prevalence of CEW infestation and the associated fumonisin contamination in A. flavus resistant maize lines. Further, delayed flowering of the two resistant maize lines might have contributed to the pervasive H. zea damage of these lines by providing young silk for egg-laying. These results highlight the need for integrated strategies targeting mycotoxigenic fungi as well as their insect vectors for enhanced food safety.
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Affiliation(s)
- Subbaiah Chalivendra
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA, United States
| | - Fangneng Huang
- Department of Entomology, Louisiana State University AgCenter, Baton Rouge, LA, United States
| | - Mark Busman
- Bacterial Foodborne Pathogens and Mycology Research Unit, USDA-ARS-NCAUR, Peoria, IL, United States
| | - W. Paul Williams
- Corn Host Plant Resistance Research Unit, USDA-ARS, Mississippi State, MS, United States
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA, United States
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Chalivendra S, DeRobertis C, Reyes Pineda J, Ham JH, Damann K. Rice Phyllosphere Bacillus Species and Their Secreted Metabolites Suppress Aspergillus flavus Growth and Aflatoxin Production In Vitro and In Maize Seeds. Toxins (Basel) 2018; 10:toxins10040159. [PMID: 29659522 PMCID: PMC5923325 DOI: 10.3390/toxins10040159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/09/2018] [Accepted: 04/11/2018] [Indexed: 12/15/2022] Open
Abstract
The emergence of super-toxigenic strains by recombination is a risk from an intensive use of intraspecific aflatoxin (AF) biocontrol agents (BCAs). Periodical alternation with interspecific-BCAs will be safer since they preclude recombination. We are developing an AF-biocontrol system using rice-associated Bacilli reported previously (RABs). More than 50% of RABs inhibited the growth of multiple A. flavus strains, with RAB4R being the most inhibitory and RAB1 among the least. The fungistatic activity of RAB4R is associated with the lysis of A. flavus hyphal tips. In field trails with the top five fungistatic RABs, RAB4R consistently inhibited AF contamination of maize by Tox4, a highly toxigenic A. flavus strain from Louisiana corn fields. RAB1 did not suppress A. flavus growth, but strongly inhibited AF production. Total and HPLC-fractionated lipopeptides (LPs) isolated from culture filtrates of RAB1 and RAB4R also inhibited AF accumulation. LPs were stable in vitro with little loss of activity even after autoclaving, indicating their potential field efficacy as a tank-mix application. A. flavus colonization and AF were suppressed in RAB1- or RAB4R-coated maize seeds. Since RAB4R provided both fungistatic and strong anti-mycotoxigenic activities in the laboratory and field, it can be a potent alternative to atoxigenic A. flavus strains. On the other hand, RAB1 may serve as an environmentally safe helper BCA with atoxigenic A. flavus strains, due its lack of strong fungistatic and hemolytic activities.
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Affiliation(s)
- Subbaiah Chalivendra
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA 70803, USA.
| | - Catherine DeRobertis
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA 70803, USA.
| | - Jorge Reyes Pineda
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA 70803, USA.
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA 70803, USA.
| | - Kenneth Damann
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA 70803, USA.
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Ren M, Venglat P, Qiu S, Feng L, Cao Y, Wang E, Xiang D, Wang J, Alexander D, Chalivendra S, Logan D, Mattoo A, Selvaraj G, Datla R. Target of rapamycin signaling regulates metabolism, growth, and life span in Arabidopsis. Plant Cell 2012; 24:4850-74. [PMID: 23275579 PMCID: PMC3556962 DOI: 10.1105/tpc.112.107144] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Target of Rapamycin (TOR) is a major nutrition and energy sensor that regulates growth and life span in yeast and animals. In plants, growth and life span are intertwined not only with nutrient acquisition from the soil and nutrition generation via photosynthesis but also with their unique modes of development and differentiation. How TOR functions in these processes has not yet been determined. To gain further insights, rapamycin-sensitive transgenic Arabidopsis thaliana lines (BP12) expressing yeast FK506 Binding Protein12 were developed. Inhibition of TOR in BP12 plants by rapamycin resulted in slower overall root, leaf, and shoot growth and development leading to poor nutrient uptake and light energy utilization. Experimental limitation of nutrient availability and light energy supply in wild-type Arabidopsis produced phenotypes observed with TOR knockdown plants, indicating a link between TOR signaling and nutrition/light energy status. Genetic and physiological studies together with RNA sequencing and metabolite analysis of TOR-suppressed lines revealed that TOR regulates development and life span in Arabidopsis by restructuring cell growth, carbon and nitrogen metabolism, gene expression, and rRNA and protein synthesis. Gain- and loss-of-function Ribosomal Protein S6 (RPS6) mutants additionally show that TOR function involves RPS6-mediated nutrition and light-dependent growth and life span in Arabidopsis.
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Affiliation(s)
- Maozhi Ren
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Prakash Venglat
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Shuqing Qiu
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Li Feng
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Yongguo Cao
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Edwin Wang
- Computational Chemistry and Bioinformatics Group, Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec H4P 2R2, Canada
| | - Daoquan Xiang
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Jinghe Wang
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | | | | | - David Logan
- Université d’Angers, Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, LUNAM Université, Angers cedex 1, France
| | - Autar Mattoo
- Sustainable Agricultural Systems Laboratory, U.S. Department of Agriculture–Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, Maryland 20705-2350
| | - Gopalan Selvaraj
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Raju Datla
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
- Address correspondence to
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