1
|
Gleason LU, Fekete FJ, Tanner RL, Dowd WW. Multi-omics reveals largely distinct transcript- and protein-level responses to the environment in an intertidal mussel. J Exp Biol 2023; 226:jeb245962. [PMID: 37902141 PMCID: PMC10690110 DOI: 10.1242/jeb.245962] [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: 04/14/2023] [Accepted: 10/12/2023] [Indexed: 10/31/2023]
Abstract
Organismal responses to stressful environments are influenced by numerous transcript- and protein-level mechanisms, and the relationships between expression changes at these levels are not always straightforward. Here, we used paired transcriptomic and proteomic datasets from two previous studies from gill of the California mussel, Mytilus californianus, to explore how simultaneous transcript and protein abundance patterns may diverge under different environmental scenarios. Field-acclimatized mussels were sampled from two disparate intertidal sites; individuals from one site were subjected to three further treatments (common garden, low-intertidal or high-intertidal outplant) that vary in temperature and feeding time. Assessing 1519 genes shared between the two datasets revealed that both transcript and protein expression patterns differentiated the treatments at a global level, despite numerous underlying discrepancies. There were far more instances of differential expression between treatments in transcript only (1451) or protein only (226) than of the two levels shifting expression concordantly (68 instances). Upregulated expression of cilium-associated transcripts (likely related to feeding) was associated with relatively benign field treatments. In the most stressful treatment, transcripts, but not proteins, for several molecular chaperones (including heat shock proteins and endoplasmic reticulum chaperones) were more abundant, consistent with a threshold model for induction of translation of constitutively available mRNAs. Overall, these results suggest that the relative importance of transcript- and protein-level regulation (translation and/or turnover) differs among cellular functions and across specific microhabitats or environmental contexts. Furthermore, the degree of concordance between transcript and protein expression can vary across benign versus acutely stressful environmental conditions.
Collapse
Affiliation(s)
- Lani U. Gleason
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA 95819, USA
| | - Florian J. Fekete
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA 95819, USA
| | - Richelle L. Tanner
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | - W. Wesley Dowd
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| |
Collapse
|
2
|
Félix JW, Granados-Alegría MI, Gómez-Tah R, Tzec-Simá M, Ruíz-May E, Canto-Canché B, Zamora-Briseño JA, Bojórquez-Velázquez E, Oropeza-Salín C, Islas-Flores I. Proteome Landscape during Ripening of Solid Endosperm from Two Different Coconut Cultivars Reveals Contrasting Carbohydrate and Fatty Acid Metabolic Pathway Modulation. Int J Mol Sci 2023; 24:10431. [PMID: 37445609 DOI: 10.3390/ijms241310431] [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: 05/23/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Cocos nucifera L. is a crop grown in the humid tropics. It is grouped into two classes of varieties: dwarf and tall; regardless of the variety, the endosperm of the coconut accumulates carbohydrates in the early stages of maturation and fatty acids in the later stages, although the biochemical factors that determine such behavior remain unknown. We used tandem mass tagging with synchronous precursor selection (TMT-SPS-MS3) to analyze the proteomes of solid endosperms from Yucatan green dwarf (YGD) and Mexican pacific tall (MPT) coconut cultivars. The analysis was conducted at immature, intermediate, and mature development stages to better understand the regulation of carbohydrate and lipid metabolisms. Proteomic analyses showed 244 proteins in YGD and 347 in MPT; from these, 155 proteins were shared between both cultivars. Furthermore, the proteomes related to glycolysis, photosynthesis, and gluconeogenesis, and those associated with the biosynthesis and elongation of fatty acids, were up-accumulated in the solid endosperm of MPT, while in YGD, they were down-accumulated. These results support that carbohydrate and fatty acid metabolisms differ among the developmental stages of the solid endosperm and between the dwarf and tall cultivars. This is the first proteomics study comparing different stages of maturity in two contrasting coconut cultivars and may help in understanding the maturity process in other palms.
Collapse
Affiliation(s)
- Jean Wildort Félix
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - María Inés Granados-Alegría
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Rufino Gómez-Tah
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Miguel Tzec-Simá
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Eliel Ruíz-May
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Colonia El Haya, Xalapa C.P. 91073, Veracruz, Mexico
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Jesús Alejandro Zamora-Briseño
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Colonia El Haya, Xalapa C.P. 91073, Veracruz, Mexico
| | - Esaú Bojórquez-Velázquez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Colonia El Haya, Xalapa C.P. 91073, Veracruz, Mexico
| | - Carlos Oropeza-Salín
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| |
Collapse
|
3
|
Cheng P, Wang C, Zhang L, Fei C, Liu Y, Wang M, Zhang K, Wang X, Gu F, Xue F. Label-free quantitative proteomic analysis of ethanamizuril-resistant versus -sensitive strains of Eimeria tenella. Parasit Vectors 2022; 15:319. [PMID: 36076292 PMCID: PMC9454127 DOI: 10.1186/s13071-022-05412-6] [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: 04/28/2022] [Accepted: 07/23/2022] [Indexed: 11/18/2022] Open
Abstract
Background Avian coccidiosis is an important parasitic disease that has serious adverse effects on the global poultry industry. The extensive use of anticoccidial drugs has resulted in an increase in drug resistance. Ethanamizuril (EZL) is a novel triazine with high anticoccidial activity. Methods We compared oocyst production and sporulation between EZL-sensitive (S) and EZL-resistant Eimeria tenella strains (R10 and R200) and used label-free quantitative proteomics to identify differentially expressed proteins (DEPs) between these strains. Results We generated two EZL-resistant E. tenella strains: strain R10, which was induced using a constant dose of 10 mg EZL/kg poultry feed, and strain R200, which was generated by gradually increasing the EZL dosage to 200 mg EZL/kg poultry feed. With an increase in resistance, the total oocyst output decreased, but the percentage of sporulation did not change significantly. We identified a total of 7511 peptides and 1282 proteins, and found 152 DEPs in the R10 strain versus the S strain, 426 DEPs in the R200 strain versus the S strain and 494 DEPs in the R200 strain versus the R10 strain. When compared with the S strain, 86 DEPs were found to have consistent trends in both resistant strains. The DEPs were primarily involved in ATP and GTP binding, invasion, and membrane components. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of the DEPs suggested that they are involved in transcription and translation processes. Protein–protein interaction network analysis of the 86 DEPs showed that 10 proteins were hubs in the functional interaction network (≥ 8 edges) and five of them were ribosomal proteins. Conclusions The results of the present study indicate that the resistance mechanisms of E. tenella against EZL might be related to the transcriptional and translational processes, especially in the factors that inhibit the growth of parasites. The DEPs found in this study provide new insights into the resistance mechanisms of E. tenella against EZL. Further research on these potential targets holds promise for new chemotherapeutic approaches for controlling E. tenella infections. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05412-6.
Collapse
Affiliation(s)
- Peipei Cheng
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Chunmei Wang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China.
| | - Lifang Zhang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Chenzhong Fei
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Yingchun Liu
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Mi Wang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Keyu Zhang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Xiaoyang Wang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Feng Gu
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Feiqun Xue
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China.
| |
Collapse
|
4
|
Yao M, Wang R, Chen Y, He P, Wei E, Zhu F, Wang Q, Zhang Y, Tang X, Shen Z. Identification and subcellular localization analysis of CCTα in microsporidian Nosema bombycis. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 102:105309. [PMID: 35636694 DOI: 10.1016/j.meegid.2022.105309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/15/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
CCT is a chaperonin which is widely present in eukaryotic cells and mainly involves in the folding and assembly of cytoskeletal proteins β-tubulin and actin. The alpha subunit of CCT(CCTα) plays a pivotal role in the folding and assembly of cytoskeletal protein(s) as an individuals or complexes. In this study, we report cloning, characterization and expression of the CCTα of Nosema bombycis (NbCCTα) for the first time. The NbCCTα gene contains a complete ORF of 1629 bp in length that encodes a 542-amino acid polypeptide. The NbCCTα is 59.662 kDa molecular weight in size with an isoelectric point (pI) of 5.81, no signal peptide or transmembrane domain. The IFA results showed that the NbCCTα was co-localized with actin and β-tubulin in the cytoplasm, nucleus, nuclear membrane and plasma membrane of N. bombycis in the process of proliferation. qPCR analysis showed that the relative expression level of NbCCTα increased from 24 h to 96 h post-infection (hp.i) of N. bombycis, and reached the highest at 96 hp.i. The relative expression level of NbCCTα gene after RNAi was restrained at a low level from 48 hp.i to 96 hp.i. Knockdown of NbCCTα gene down-regulated the expression of Nbβ-tubulin and Nbactin genes. These results imply that NbCCTα may play an important role in the lifecycle of N. bombycis.
Collapse
Affiliation(s)
- Mingshuai Yao
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Jiangsu Collage of Tourism, Yangzhou 215000, Jiangsu Province, China
| | - Runpeng Wang
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Ying Chen
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Ping He
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Erjun Wei
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Feng Zhu
- College of Life Sciences, Zaozhuang University, Zaozhuang 277160, Shandong Province, China
| | - Qiang Wang
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, Jiangsu Province, China
| | - Yiling Zhang
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, Jiangsu Province, China
| | - Xudong Tang
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, Jiangsu Province, China
| | - Zhongyuan Shen
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, Jiangsu Province, China.
| |
Collapse
|
5
|
Park JC, Lee JS. Genome-wide identification of heat shock proteins in harpacticoid, cyclopoid, and calanoid copepods: Potential application in marine ecotoxicology. MARINE POLLUTION BULLETIN 2021; 169:112545. [PMID: 34111604 DOI: 10.1016/j.marpolbul.2021.112545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Constant evolution of omics-technologies has provided access to identification of various important gene families. Recently, genome assemblies on widely used ecotoxicological model species, including rotifers and copepods have been completed and representative detoxification-related gene families have been discovered for biomarker genes. However, despite ubiquitous presence of stress-response proteins, limited information on full genome-wide report on heat shock proteins (Hsps) is available. Various studies have demonstrated multiple cellular functions of Hsps in living organisms as an important biomarker in response to abiotic and biotic stressors, however, full genome-wide identification of Hsps, particularly in aquatic invertebrates, has not been reported. This is the first study to report the entire Hsps and basal gene expression levels in three regional-specific copepods: Tigriopus japonicus and kingsejongensis, Paracyclopina nana, and Eurytemora affnis, and how each Hsp family gene is regulated at a basal level.
Collapse
Affiliation(s)
- Jun Chul Park
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| |
Collapse
|
6
|
Zhang D, Zhao P, Liu J, Qi T, Liu Q, Jiang S, Zhang H, Wang Z, Tang B, Ding G. Transcriptome Analysis Reveals the Tolerance Mechanism of Mantis Shrimp ( Oratosquilla oratoria) under a Lipopolysaccharide Challenge. ACS OMEGA 2020; 5:2310-2317. [PMID: 32064393 PMCID: PMC7017407 DOI: 10.1021/acsomega.9b03629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/16/2020] [Indexed: 05/12/2023]
Abstract
Lipopolysaccharide (LPS), a major cell wall component of Gram-negative bacteria, is considered to lead to some disease development in commercial crustaceans. However, mantis shrimps Oratosquilla oratoria (Crustacea: Stomatopoda) have a strong vitality and ability to resist disease. To study the tolerance mechanism of mantis shrimp, transcriptome analyses were conducted in hepatopancreas of O. oratoria under LPS challenge investigation. Totally, 84 547 044 clean reads were obtained from transcriptomes (43 159 230 in OP (control), 41 387 814 in OL (treatment), respectively). Unigenes, the longest transcript of each gene, with a total length of 68 318 880 bp and the total number of 100 978 were obtained. 8369 (8.28%) of unigenes were successfully annotated in all databases and 54 888 (54.35%) were annotated in at least one database. Finally, 1012 differentially expressed genes (DEGs) including 439 and 573 showed significantly upregulated and downregulated were determined between OL and OP, respectively. Moreover, those DEGs only expressed in OL or OP accounted for 8.99%. The functional classification based on GO and KEGG indicated that the common enrichment categories for the DEGs are "amino sugar metabolic" and "cellular homeostasis" and that the progress of nutrient metabolic and homeostasis in cells is important in facing variable environmental conditions. Protein-protein interaction analysis elucidated proteins, β-actin (ACTB_G1), T-complex protein subunits (TCPs), heat shock proteins (HSPs), hydroxysteroid dehydrogenase-like protein 2 (HSDL2), kinesin family member 5 (KIF5), methylglutaconyl-CoA hydratase (AUH), and myosin heavy chain (MYH) may play key roles in response to an LPS challenge. This study laid a foundation to further investigate the possible adaptation way that O. oratoria survives in a bacterial challenge.
Collapse
Affiliation(s)
- Daizhen Zhang
- Jiangsu
Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial
Key Laboratory of Coastal Wetland Bioresources and Environmental Protection,
Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China
| | - Peisong Zhao
- Jiangsu
Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial
Key Laboratory of Coastal Wetland Bioresources and Environmental Protection,
Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Jun Liu
- Key
Laboratory of Biotechnology in Lianyungang Normal College, Lianyungang 222006, China
| | - Tingting Qi
- Jiangsu
Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial
Key Laboratory of Coastal Wetland Bioresources and Environmental Protection,
Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China
| | - Qiuning Liu
- Jiangsu
Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial
Key Laboratory of Coastal Wetland Bioresources and Environmental Protection,
Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China
| | - Senhao Jiang
- Jiangsu
Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial
Key Laboratory of Coastal Wetland Bioresources and Environmental Protection,
Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China
| | - Huabin Zhang
- Jiangsu
Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial
Key Laboratory of Coastal Wetland Bioresources and Environmental Protection,
Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China
| | - Zhengfei Wang
- Jiangsu
Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial
Key Laboratory of Coastal Wetland Bioresources and Environmental Protection,
Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China
| | - Boping Tang
- Jiangsu
Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial
Key Laboratory of Coastal Wetland Bioresources and Environmental Protection,
Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China
| | - Ge Ding
- Chemical
and Biological Engineering College, Yancheng
Institute of Technology, Yancheng 224003, China
| |
Collapse
|