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Li H, Gao S, Shi S, Zhao X, Ye H, Luo Y. Rational construction of genome-minimized Streptomyces host for the expression of secondary metabolite gene clusters. Synth Syst Biotechnol 2024; 9:600-608. [PMID: 38774831 PMCID: PMC11106782 DOI: 10.1016/j.synbio.2024.04.017] [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: 02/04/2024] [Revised: 04/16/2024] [Accepted: 04/29/2024] [Indexed: 05/24/2024] Open
Abstract
Streptomyces offer a wealth of naturally occurring compounds with diverse structures, many of which possess significant pharmaceutical values. However, new product exploration and increased yield of specific compounds in Streptomyces have been technically challenging due to their slow growth rate, complex culture conditions and intricate genetic backgrounds. In this study, we screened dozens of Streptomyces strains inhabiting in a plant rhizosphere for fast-growing candidates, and further employed CRISPR/Cas-based engineering techniques for stepwise refinement of a particular strain, Streptomyces sp. A-14 that harbors a 7.47 Mb genome. After strategic removal of nonessential genomic regions and most gene clusters, we reduced its genome size to 6.13 Mb, while preserving its growth rate to the greatest extent. We further demonstrated that cleaner metabolic background of this engineered strain was well suited for the expression and characterization of heterologous gene clusters, including the biosynthetic pathways of actinorhodin and polycyclic tetramate macrolactams. Moreover, this streamlined genome is anticipated to facilitate directing the metabolic flux towards the production of desired compounds and increasing their yields.
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Affiliation(s)
- Hui Li
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Sheng Gao
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Sanyuan Shi
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Xiaomin Zhao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Haoyu Ye
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yunzi Luo
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Tangxing Road 133, Nanshan District, Shenzhen, 518071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
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2
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Li M, Yan S, Feng X, Jiang Q, Guan M, Shen J, Liu Z. An upstream signaling gene calmodulin regulates the synthesis of insect wax via activating fatty acid biosynthesis pathway. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024; 169:104126. [PMID: 38663758 DOI: 10.1016/j.ibmb.2024.104126] [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: 02/14/2024] [Revised: 04/09/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024]
Abstract
Insect wax accumulates on the surface of insect cuticle, which acts as an important protective barrier against rain, ultraviolet light radiation, pathogens, etc. The waxing behavior, wax composition and molecular mechanism underling wax biosynthesis are unclear in dustywings. Herein, the current study determined the vital developmental stage for waxing behavior in dustywings, examined the components of waxy secretions, and identified key regulatory genes for wax biosynthesis. The wax glands were mainly located on the thorax and abdomen of dustywing adults. The adults spread the waxy secretions over their entire body surface. The metabolomics analysis identified 32 lipids and lipid-like molecules, 15 organic acids and derivatives, 7 benzenoids, etc. as the main components of waxy secretions. The fatty acids represented the largest proportion of the category of lipid and lipid-like molecules. The conjoint analysis of metabolomics and transcriptomics identified two crucial genes fatty acyl-CoA reductase (CsFAR) and calmodulin (CsCaM) for wax biosynthesis. The down-regulation of these genes via nanocarrier-mediated RNA interference technology significantly reduced the amount of wax particles. Notably, the RNAi of CsCaM apparently suppressed the expression of most genes in fatty acid biosynthesis pathway, indicating the CsCaM might act as a main upstream regulator of fatty acid biosynthesis pathway.
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Affiliation(s)
- Min Li
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Shuo Yan
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Xinying Feng
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Qinhong Jiang
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Mei Guan
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Jie Shen
- College of Plant Protection, China Agricultural University, Beijing, 100193, China.
| | - Zhiqi Liu
- College of Plant Protection, China Agricultural University, Beijing, 100193, China.
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Bai S, Huang Z, Li XG. Genome analysis of Rossellomorea sp. y25, a deep sea bacterium isolated from the sediments of South China Sea. Mar Genomics 2024; 75:101110. [PMID: 38735673 DOI: 10.1016/j.margen.2024.101110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/19/2024] [Accepted: 04/19/2024] [Indexed: 05/14/2024]
Abstract
Rossellomorea sp. y25, a putative new species of yellow pigment-producing, aerobic and chemoheterotrophic bacterium belonging to the family Bacillaceae, was isolated from the sediments at the depth of 1829 m in the South China Sea. In this study, we present the complete genome sequences of strain y25, which consisted of only one circular chromosome with 4,633,006 bp and the content of G + C was 41.76%. A total of 4466 CDSs, 106 tRNA, 33 rRNA, and 101 sRNA genes were obtained. Genomic analysis of strain y25 showed that it has the ability to produce antioxidant carotenoids and a large number of heavy metal resistance genes, such as arsenic, cadmium and zinc. In addition, strain y25 contains a prophage that may contribute to host protection against lysis by related Bacillus-like phages. This is the first report of genome-wide information on a bacterium of the genus Rossellomorea isolated from the deep sea, providing insights into how microorganisms of this genus adapt to deep-sea environments.
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Affiliation(s)
- Shijie Bai
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Zhaosong Huang
- School of Biological Science and Technology, University of Jinan, Jinan 250024, China
| | - Xue-Gong Li
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
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4
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Li X, Zhang X, Zhang M, Luo X, Zhang T, Liu X, Lu R, Zhang Y. Environmental magnesium ion affects global gene expression, motility, biofilm formation and virulence of Vibrio parahaemolyticus. Biofilm 2024; 7:100194. [PMID: 38577556 PMCID: PMC10990858 DOI: 10.1016/j.bioflm.2024.100194] [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: 02/02/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Vibrio parahaemolyticus is widely distributed in marine ecosystems. Magnesium ion (Mg2+) is the second most abundant metal cation in seawater, and plays important roles in the growth and gene expression of V. parahaemolyticus, but lacks the detailed mechanisms. In this study, the RNA sequencing data demonstrated that a total of 1494 genes was significantly regulated by Mg2+. The majority of the genes associated with lateral flagella, exopolysaccharide, type III secretion system 2, type VI secretion system (T6SS) 1, T6SS2, and thermostable direct hemolysin were downregulated. A total of 18 genes that may be involved in c-di-GMP metabolism and more than 80 genes encoding putative regulators were also significantly and differentially expressed in response to Mg2+, indicating that the adaptation process to Mg2+ stress may be strictly regulated by complex regulatory networks. In addition, Mg2+ promoted the proliferative speed, swimming motility and cell adhesion of V. parahaemolyticus, but inhibited the swarming motility, biofilm formation, and c-di-GMP production. However, Mg2+ had no effect on the production of capsular polysaccharide and cytoxicity against HeLa cells. Therefore, Mg2+ had a comprehensive impact on the physiology and gene expression of V. parahaemolyticus.
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Affiliation(s)
- Xue Li
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China
| | - Xiaobai Zhang
- Department of Respiratory Medicine, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China
| | - Miaomiao Zhang
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China
| | - Xi Luo
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China
| | - Tingting Zhang
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China
| | - Xianjin Liu
- Department of Infection, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China
| | - Renfei Lu
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China
| | - Yiquan Zhang
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China
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Wu-Chuang A, Mateos-Hernandez L, Abuin-Denis L, Maitre A, Avellanet J, García A, Fuentes D, Cabezas-Cruz A. Exploring the impact of breast cancer on colonization resistance of mouse microbiota using network node manipulation. Heliyon 2024; 10:e30914. [PMID: 38784541 PMCID: PMC11112314 DOI: 10.1016/j.heliyon.2024.e30914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 04/11/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Breast cancer, a global health concern affecting women, has been linked to alterations in the gut microbiota, impacting various aspects of human health. This study investigates the interplay between breast cancer and the gut microbiome, particularly focusing on colonization resistance-an essential feature of the microbiota's ability to prevent pathogenic overgrowth. Using a mouse model of breast cancer, we employ diversity analysis, co-occurrence network analysis, and robustness tests to elucidate the impact of breast cancer on microbiome dynamics. Our results reveal that breast cancer exposure affects the bacterial community's composition and structure, with temporal dynamics playing a role. Network analysis demonstrates that breast cancer disrupts microbial interactions and decreases network complexity, potentially compromising colonization resistance. Moreover, network robustness analysis shows the susceptibility of the microbiota to node removal, indicating potential vulnerability to pathogenic colonization. Additionally, predicted metabolic profiling of the microbiome highlights the significance of the enzyme EC 6.2.1.2 - Butyrate--CoA ligase, potentially increasing butyrate, and balancing the reduction of colonization resistance. The identification of Rubrobacter as a key contributor to this enzyme suggests its role in shaping the microbiota's response to breast cancer. This study uncovers the intricate relationship between breast cancer, the gut microbiome, and colonization resistance, providing insights into potential therapeutic strategies and diagnostic approaches for breast cancer patients.
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Affiliation(s)
- Alejandra Wu-Chuang
- Anses, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
| | - Lourdes Mateos-Hernandez
- Anses, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
| | - Lianet Abuin-Denis
- Anses, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology, Avenue 31 between 158 and 190, P.O. Box 6162, 10600, Havana, Cuba
| | - Apolline Maitre
- Anses, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
- INRAE, UR 0045 Laboratoire de Recherches Sur Le Développement de L'Elevage (SELMET-LRDE), Corte, France
- EA 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Janet Avellanet
- Center of Molecular Immunology (CIM), Calle 15 esq. 216, Atabey, Playa, Havana, Cuba
| | - Arlem García
- Center of Molecular Immunology (CIM), Calle 15 esq. 216, Atabey, Playa, Havana, Cuba
| | - Dasha Fuentes
- National Center for Laboratory Animal Breeding (CENPALAB), Calle 3ra # 40759 entre 6ta y carretera de Tirabeque, Rpto La Unión, Boyeros, Havana, Cuba
| | - Alejandro Cabezas-Cruz
- Anses, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
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Zhang C, Li Z, Sun T, Zang S, Wang D, Su Y, Wu Q, Que Y. Sugarcane ScCAX4 is a Negative Regulator of Resistance to Pathogen Infection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38809782 DOI: 10.1021/acs.jafc.4c00805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Calcium (Ca2+) is a second messenger in various physiological processes within plants. The significance of the Ca2+/H+ exchanger (CAX) has been established in facilitating Ca2+ transport in plants; however, disease resistance functions of the CAX gene remain elusive. In this study, we conducted sequence characterization and expression analysis for a sugarcane CAX gene, ScCAX4 (GenBank Accession Number: MW206380). In order to further investigate the disease resistance functions, this gene was then transiently overexpressed in Nicotiana benthamiana leaves, which were subsequently inoculated with Fusarium solani var. coeruleum. Results showed that ScCAX4 overexpression increased the susceptibility of N. benthamiana to pathogen infection by regulating the expression of genes related to salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) pathways, suggesting its negative role in disease resistance. Furthermore, we genetically transformed the ScCAX4 gene into N. benthamiana and obtained three positive T2 generation lines. Interestingly, the symptomatology of transgenic plants was consistent with that of transient overexpression after pathogen inoculation. Notably, the JA content in transgenic overexpression lines was significantly higher than that in the wild-type. RNA-seq revealed that ScCAX4 could mediate multiple signaling pathways, and the JA signaling pathway played a key role in modulating disease resistance. Finally, a regulatory model was depicted for the increased susceptibility to pathogen infection conferred by the ScCAX4 gene. This study provides genetic resources for sugarcane molecular breeding and the research direction for plant CAX genes.
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Affiliation(s)
- Chang Zhang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhenxiang Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tingting Sun
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qibin Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Youxiong Que
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou, 571101 Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Rebhi S, Basharat Z, Wei CR, Lebbal S, Najjaa H, Sadfi-Zouaoui N, Messaoudi A. Core proteome mediated subtractive approach for the identification of potential therapeutic drug target against the honeybee pathogen Paenibacillus larvae. PeerJ 2024; 12:e17292. [PMID: 38818453 PMCID: PMC11138523 DOI: 10.7717/peerj.17292] [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: 11/16/2023] [Accepted: 04/02/2024] [Indexed: 06/01/2024] Open
Abstract
Background & Objectives American foulbrood (AFB), caused by the highly virulent, spore-forming bacterium Paenibacillus larvae, poses a significant threat to honey bee brood. The widespread use of antibiotics not only fails to effectively combat the disease but also raises concerns regarding honey safety. The current computational study was attempted to identify a novel therapeutic drug target against P. larvae, a causative agent of American foulbrood disease in honey bee. Methods We investigated effective novel drug targets through a comprehensive in silico pan-proteome and hierarchal subtractive sequence analysis. In total, 14 strains of P. larvae genomes were used to identify core genes. Subsequently, the core proteome was systematically narrowed down to a single protein predicted as the potential drug target. Alphafold software was then employed to predict the 3D structure of the potential drug target. Structural docking was carried out between a library of phytochemicals derived from traditional Chinese flora (n > 36,000) and the potential receptor using Autodock tool 1.5.6. Finally, molecular dynamics (MD) simulation study was conducted using GROMACS to assess the stability of the best-docked ligand. Results Proteome mining led to the identification of Ketoacyl-ACP synthase III as a highly promising therapeutic target, making it a prime candidate for inhibitor screening. The subsequent virtual screening and MD simulation analyses further affirmed the selection of ZINC95910054 as a potent inhibitor, with the lowest binding energy. This finding presents significant promise in the battle against P. larvae. Conclusions Computer aided drug design provides a novel approach for managing American foulbrood in honey bee populations, potentially mitigating its detrimental effects on both bee colonies and the honey industry.
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Affiliation(s)
- Sawsen Rebhi
- Université de Tunis-El Manar, Laboratoire de Mycologie, Pathologies et Biomarqueurs, Département de Biologie, Tunis, Tunisia
| | | | - Calvin R. Wei
- Department of Research and Development, Shing Huei Group, Taipei, Taiwan
| | - Salim Lebbal
- University of Khenchela, Department of Agricultural Sciences, Faculty of Nature and Life Sciences, Khenchela, Algeria
| | - Hanen Najjaa
- University of Gabes, Laboratory of Pastoral Ecosystem and Valorization of Spontaneous Plants and Associated Microorganisms, Institute of Arid Lands of Medenine, Medenine, Tunisia
| | - Najla Sadfi-Zouaoui
- Université de Tunis-El Manar, Laboratoire de Mycologie, Pathologies et Biomarqueurs, Département de Biologie, Tunis, Tunisia
| | - Abdelmonaem Messaoudi
- Université de Tunis-El Manar, Laboratoire de Mycologie, Pathologies et Biomarqueurs, Département de Biologie, Tunis, Tunisia
- Jendouba University, Higher Institute of Biotechnology of Beja, Beja, Tunisia
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8
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Li Z, Liu D, Wang D, Sun M, Zhang G, Wu Y, Zhang Y, Cheng B. Study on the causes of changes in colour during Hibiscus syriacus flowering based on transcriptome and metabolome analyses. BMC PLANT BIOLOGY 2024; 24:431. [PMID: 38773421 PMCID: PMC11107057 DOI: 10.1186/s12870-024-05142-0] [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: 08/07/2023] [Accepted: 05/13/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND The flower colour of H. syriacus 'Qiansiban' transitions from fuchsia to pink-purple and finally to pale purple, thereby enhancing the ornamental value of the cultivars. However, the molecular mechanism underlying this change in flower colour in H. syriacus has not been elucidated. In this study, the transcriptomic data of H. syriacus 'Qiansiban' at five developmental stages were analysed to investigate the impact of flavonoid components on flower colour variation. Additionally, five cDNA libraries were constructed from H. syriacus 'Qiansiban' during critical blooming stages, and the transcriptomes were sequenced to investigate the molecular mechanisms underlying changes in flower colouration. RESULTS High-performance liquid chromatography‒mass spectrometry detected five anthocyanins in H. syriacus 'Qiansiban', with malvaccin-3-O-glucoside being the predominant compound in the flowers of H. syriacus at different stages, followed by petunigenin-3-O-glucoside. The levels of these five anthocyanins exhibited gradual declines throughout the flowering process. In terms of the composition and profile of flavonoids and flavonols, a total of seven flavonoids were identified: quercetin-3-glucoside, luteolin-7-O-glucoside, Santianol-7-O-glucoside, kaempferol-O-hexosyl-C-hexarbonoside, apigenin-C-diglucoside, luteolin-3,7-diglucoside, and apigenin-7-O-rutinoside. A total of 2,702 DEGs were identified based on the selected reference genome. Based on the enrichment analysis of differentially expressed genes, we identified 9 structural genes (PAL, CHS, FLS, DRF, ANS, CHI, F3H, F3'5'H, and UFGT) and 7 transcription factors (3 MYB, 4 bHLH) associated with flavonoid biosynthesis. The qRT‒PCR results were in good agreement with the high-throughput sequencing data. CONCLUSION This study will establish a fundamental basis for elucidating the mechanisms underlying alterations in the flower pigmentation of H. syriacus.
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Affiliation(s)
- Zhezhe Li
- Hebei Normal University of Science & Technology, Qinhuangdao, 066004, Hebei Province, China
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Qinghuangdao, 066004, Hebe Province, China
- Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Hebei Normal University of Science & Technology, Qinhuangdao Hebei Province, Qinhuangdao, 066004, Hebe Province, China
| | - Dan Liu
- Shandong Provincial Forest and Grass Germplasm Resources Center, Jinan, 250102, Shangdong Province, China
| | - Dongsheng Wang
- Hebei Normal University of Science & Technology, Qinhuangdao, 066004, Hebei Province, China
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Qinghuangdao, 066004, Hebe Province, China
- Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Hebei Normal University of Science & Technology, Qinhuangdao Hebei Province, Qinhuangdao, 066004, Hebe Province, China
| | - Meng Sun
- Hebei Normal University of Science & Technology, Qinhuangdao, 066004, Hebei Province, China
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Qinghuangdao, 066004, Hebe Province, China
| | - Guojun Zhang
- Hebei Normal University of Science & Technology, Qinhuangdao, 066004, Hebei Province, China
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Qinghuangdao, 066004, Hebe Province, China
- Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Hebei Normal University of Science & Technology, Qinhuangdao Hebei Province, Qinhuangdao, 066004, Hebe Province, China
| | - Yu Wu
- Hebei Normal University of Science & Technology, Qinhuangdao, 066004, Hebei Province, China
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Qinghuangdao, 066004, Hebe Province, China
| | - Yidan Zhang
- Hebei Normal University of Science & Technology, Qinhuangdao, 066004, Hebei Province, China
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Qinghuangdao, 066004, Hebe Province, China
| | - Beibei Cheng
- Hebei Normal University of Science & Technology, Qinhuangdao, 066004, Hebei Province, China.
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Qinghuangdao, 066004, Hebe Province, China.
- Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Hebei Normal University of Science & Technology, Qinhuangdao Hebei Province, Qinhuangdao, 066004, Hebe Province, China.
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9
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Stajich JE, Lovett B, Lee E, Macias AM, Hajek AE, de Bivort BL, Kasson MT, De Fine Licht HH, Elya C. Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi. eLife 2024; 12:RP92863. [PMID: 38767950 PMCID: PMC11105155 DOI: 10.7554/elife.92863] [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] [Indexed: 05/22/2024] Open
Abstract
Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. In this manuscript, we present a genome for a laboratory-tractable Entomophthora muscae isolate that infects fruit flies. Our E. muscae assembly is 1.03 Gb, consists of 7810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with recent datasets from entomophthoralean fungi, we show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity. In addition, we find that E. muscae and its closest allies possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae's species-specific, biotrophic lifestyle. Finally, we offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex that support the need for taxonomic revision within this group. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.
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Affiliation(s)
- Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-RiversideRiversideUnited States
| | - Brian Lovett
- Emerging Pests and Pathogens Research Unit, USDA-ARSIthacaUnited States
| | - Emily Lee
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Angie M Macias
- Division of Plant and Soil Sciences, West Virginia UniversityMorgantownUnited States
| | - Ann E Hajek
- Department of Entomology, Cornell UniversityIthacaUnited States
| | - Benjamin L de Bivort
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Matt T Kasson
- Division of Plant and Soil Sciences, West Virginia UniversityMorgantownUnited States
| | - Henrik H De Fine Licht
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of CopenhagenCopenhagenDenmark
| | - Carolyn Elya
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
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10
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Zhao Q, Xiong H, Yu H, Wang C, Zhang S, Hao J, Wang J, Zhang H, Zhang L. Function of MYB8 in larch under PEG simulated drought stress. Sci Rep 2024; 14:11290. [PMID: 38760385 PMCID: PMC11101485 DOI: 10.1038/s41598-024-61510-8] [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: 03/08/2024] [Accepted: 05/07/2024] [Indexed: 05/19/2024] Open
Abstract
Larch, a prominent afforestation, and timber species in northeastern China, faces growth limitations due to drought. To further investigate the mechanism of larch's drought resistance, we conducted full-length sequencing on embryonic callus subjected to PEG-simulated drought stress. The sequencing results revealed that the differentially expressed genes (DEGs) primarily played roles in cellular activities and cell components, with molecular functions such as binding, catalytic activity, and transport activity. Furthermore, the DEGs showed significant enrichment in pathways related to protein processing, starch and sucrose metabolism, benzose-glucuronic acid interconversion, phenylpropyl biology, flavonoid biosynthesis, as well as nitrogen metabolism and alanine, aspartic acid, and glutamic acid metabolism. Consequently, the transcription factor T_transcript_77027, which is involved in multiple pathways, was selected as a candidate gene for subsequent drought stress resistance tests. Under PEG-simulated drought stress, the LoMYB8 gene was induced and showed significantly upregulated expression compared to the control. Physiological indices demonstrated an improved drought resistance in the transgenic plants. After 48 h of PEG stress, the transcriptome sequencing results of the transiently transformed LoMYB8 plants and control plants exhibited that genes were significantly enriched in biological process, cellular component and molecular function. Function analyses indicated for the enrichment of multiple KEGG pathways, including energy synthesis, metabolic pathways, antioxidant pathways, and other relevant processes. The pathways annotated by the differential metabolites mainly encompassed signal transduction, carbohydrate metabolism, amino acid metabolism, and flavonoid metabolism.
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Affiliation(s)
- Qingrong Zhao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Huanhuan Xiong
- Forestry Research Institute in Heilongjiang Province, Harbin, China
| | - Hongying Yu
- State Administration of Forestry and Grassland, Harbin Research Institute of Forestry Machinery, Harbin, China
| | - Chen Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Sufang Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Junfei Hao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding (Chinese Academy of Forestry), Beijing, China
| | - Hanguo Zhang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China.
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China.
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11
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Chen H, Sahu SK, Wang S, Liu J, Yang J, Cheng L, Chiu TY, Liu H. Chromosome-level Alstonia scholaris genome unveils evolutionary insights into biosynthesis of monoterpenoid indole alkaloids. iScience 2024; 27:109599. [PMID: 38646178 PMCID: PMC11033161 DOI: 10.1016/j.isci.2024.109599] [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: 11/17/2023] [Revised: 01/25/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Alstonia scholaris of the Apocynaceae family is a medicinal plant with a rich source of bioactive monoterpenoid indole alkaloids (MIAs), which possess anti-cancer activity like vinca alkaloids. To gain genomic insights into MIA biosynthesis, we assembled a high-quality chromosome-level genome for A. scholaris using nanopore and Hi-C data. The 444.95 Mb genome contained 35,488 protein-coding genes. A total of 20 chromosomes were assembled with a scaffold N50 of 21.75 Mb. The genome contained a cluster of strictosidine synthases and tryptophan decarboxylases with synteny to other species and a saccharide-terpene cluster involved in the monoterpenoid biosynthesis pathway of the MIA upstream pathway. The multi-omics data of A. scholaris provide a valuable resource for understanding the evolutionary origins of MIAs and for discovering biosynthetic pathways and synthetic biology efforts for producing pharmaceutically useful alkaloids.
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Affiliation(s)
- Haixia Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Shujie Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Jia Liu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Jinlong Yang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Le Cheng
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Tsan-Yu Chiu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
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12
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Wang Y, Li S, Wang T, Zou M, Peng X. Extracellular Vesicles From Mycoplasma gallisepticum: Modulators of Macrophage Activation and Virulence. J Infect Dis 2024; 229:1523-1534. [PMID: 37929888 DOI: 10.1093/infdis/jiad486] [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: 07/03/2023] [Revised: 10/21/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023] Open
Abstract
Extracellular vesicles (EVs) mediate intercellular communication by transporting proteins. To investigate the pathogenesis of Mycoplasma gallisepticum, a major threat to the poultry industry, we isolated and characterized M. gallisepticum-produced EVs. Our study highlights the significant impact of M. gallisepticum-derived EVs on immune function and macrophage apoptosis, setting them apart from other M. gallisepticum metabolites. These EVs dose-dependently enhance M. gallisepticum adhesion and proliferation, simultaneously modulating Toll-like receptor 2 and interferon γ pathways and thereby inhibiting macrophage activation. A comprehensive protein analysis revealed 117 proteins in M. gallisepticum-derived EVs, including established virulence factors, such as GapA, CrmA, VlhA, and CrmB. Crucially, these EV-associated proteins significantly contribute to M. gallisepticum infection. Our findings advance our comprehension of M. gallisepticum pathogenesis, offering insights for preventive strategies and emphasizing the pivotal role of M. gallisepticum-derived EVs and their associated proteins. This research sheds light on the composition and crucial role of M. gallisepticum-derived EVs in M. gallisepticum pathogenesis, aiding our fight against M. gallisepticum infections.
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Affiliation(s)
- Yingjie Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Shiying Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Tengfei Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Mengyun Zou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiuli Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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13
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Zhang L, Lin TY, Liu WT, Ling F. Toward Characterizing Environmental Sources of Non-tuberculous Mycobacteria (NTM) at the Species Level: A Tutorial Review of NTM Phylogeny and Phylogenetic Classification. ACS ENVIRONMENTAL AU 2024; 4:127-141. [PMID: 38765059 PMCID: PMC11100324 DOI: 10.1021/acsenvironau.3c00074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 05/21/2024]
Abstract
Nontuberculous mycobacteria (NTM) are any mycobacteria that do not cause tuberculosis or leprosy. While the majority of NTM are harmless and some of them are considered probiotic, a growing number of people are being diagnosed with NTM infections. Therefore, their detection in the environment is of interest to clinicians, environmental microbiologists, and water quality researchers alike. This review provides a tutorial on the foundational approaches for taxonomic classifications, with a focus on the phylogenetic relationships among NTM revealed by the 16S rRNA gene, rpoB gene, and hsp65 gene, and by genome-based approaches. Recent updates on the Mycobacterium genus taxonomy are also provided. A synthesis on the habitats of 189 mycobacterial species in a genome-based taxonomy framework was performed, with attention paid to environmental sources (e.g., drinking water, aquatic environments, and soil). The 16S rRNA gene-based classification accuracy for various regions was evaluated (V3, V3-V4, V3-V5, V4, V4-V5, and V1-V9), revealing overall excellent genus-level classification (up to 100% accuracy) yet only modest performance (up to 63.5% accuracy) at the species level. Future research quantifying NTM species in water systems, determining the effects of water treatment and plumbing conditions on their variations, developing high throughput species-level characterization tools for use in the environment, and incorporating the characterization of functions in a phylogenetic framework will likely fill critical knowledge gaps. We believe this tutorial will be useful for researchers new to the field of molecular or genome-based taxonomic profiling of environmental microbiomes. Experts may also find this review useful in terms of the selected key findings of the past 30 years, recent updates on phylogenomic analyses, as well as a synthesis of the ecology of NTM in a phylogenetic framework.
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Affiliation(s)
- Lin Zhang
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tzu-Yu Lin
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Wen-Tso Liu
- Department
of Civil and Environmental Engineering, University of Illinois, Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Fangqiong Ling
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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14
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Luo J, Liu M, Ai W, Zheng X, Liu S, Huang K, Zhang C, Li Q, Luo C. Synergy of lytic phage pB23 and meropenem combination against carbapenem-resistant Acinetobacter baumannii. Antimicrob Agents Chemother 2024:e0044824. [PMID: 38742904 DOI: 10.1128/aac.00448-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024] Open
Abstract
Phage-antibiotic combination treatment is a novel noteworthy drug delivery method in anti-infection. In the current study, we have isolated a new phage, pB23, against carbapenem-resistant Acinetobacter baumannii 2023. Synergistic antibacterial effect between phage pB23 and meropenem combination could be more stable, using moderate doses of phage (multiplicity of infection ranging from 0.1 to 1,000) based on results of in vitro antibacterial activity. Phage pB23 and meropenem combination could effectively clear mature biofilms and prevent biofilm formation of carbapenem-resistant Acinetobacter baumannii in vitro. Phage pB23 and meropenem combination also has good synergistic antibacterial effects against carbapenem-resistant Acinetobacter baumannii in different growth phases under static culture conditions. The pig skin explant model shows that phage pB23 and meropenem combination has a synergistic effect to remove bacteria from wounds ex vivo. Phage pB23 and meropenem combination also exhibited a synergistic antibacterial effect in vivo using a zebrafish infection mode. The potential promotion of phage proliferation by meropenem and the sensitivity recovery of phage-resistant bacteria to meropenem might elucidate the mechanism of the synergistic antimicrobial activity. In summary, our study illustrates that phage pB23 and meropenem combination could produce synergistic antibacterial effects against carbapenem-resistant Acinetobacter baumannii under static growth conditions. This study also demonstrates that phage-antibiotic combination will become an effective strategy to enhance antibacterial activity of individual drug and provide a new idea of the drug development for the treatment of infections due to carbapenem-resistant Acinetobacter baumannii and other multidrug-resistant bacteria.
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Affiliation(s)
- Jun Luo
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
- Yichang Central People's Hospital, Yichang, China
| | - Min Liu
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
- Yichang Central People's Hospital, Yichang, China
| | - Wen Ai
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
- Yichang Central People's Hospital, Yichang, China
| | - Xiaoling Zheng
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
- Yichang Central People's Hospital, Yichang, China
| | - Shaowei Liu
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
- Yichang Central People's Hospital, Yichang, China
| | - Kuo Huang
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
- Yichang Central People's Hospital, Yichang, China
| | - Changlin Zhang
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
- Yichang Central People's Hospital, Yichang, China
| | - Qianyuan Li
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
- Yichang Central People's Hospital, Yichang, China
| | - Chunhua Luo
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
- Yichang Central People's Hospital, Yichang, China
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15
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Bao Y, Deng J, Akbar S, Duan Z, Zhang C, Lin W, Wu S, Yue Y, Yao W, Xu J, Zhang M. Genome-Wide Identification and Characterization of Homeobox Transcription Factors in Phoma sorghina var. saccharum Causing Sugarcane Twisted Leaf Disease. Int J Mol Sci 2024; 25:5346. [PMID: 38791383 PMCID: PMC11121360 DOI: 10.3390/ijms25105346] [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: 04/08/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
A homeobox transcription factor is a conserved transcription factor, ubiquitous in eukaryotes, that regulates the tissue formation of structure, cell differentiation, proliferation, and cancer. This study identified the homeobox transcription factor family and its distribution in Phoma sorghina var. saccharum at the whole genome level. It elucidated the gene structures and evolutionary characteristics of this family. Additionally, knockout experiments were carried out and the preliminary function of these transcription factors was studied. Through bioinformatics approaches, nine homeobox transcription factors (PsHOX1-PsHOX9) were identified in P. sorghina var. saccharum, and these contained HOX-conserved domains and helix-turn-helix secondary structures. Nine homeobox gene deletion mutants were obtained using the homologous recombinant gene knockout technique. Protoplast transformation was mediated by polyethylene glycol (PEG) and the transformants were identified using PCR. The knockouts of PsHOX1, PsHOX2, PsHOX3, PsHOX4, PsHOX6, PsHOX8, and PsHOX9 genes resulted in a smaller growth diameter in P. sorghina var. saccharum. In contrast, the knockouts of the PsHOX3, PsHOX6, and PsHOX9 genes inhibited the formation of conidia and led to a significant decrease in the pathogenicity. This study's results will provide insights for understanding the growth and development of P. sorghina var. saccharum. The pathogenic mechanism of the affected sugarcane will provide an essential theoretical basis for preventing and controlling sugarcane twisted leaf disease.
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Affiliation(s)
- Yixue Bao
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Jinlan Deng
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Sehrish Akbar
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Zhenzhen Duan
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Chi Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Wenfeng Lin
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Suyan Wu
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Yabing Yue
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Wei Yao
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
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16
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Varela JL, Nikouli E, Medina A, Papaspyrou S, Kormas K. The gills and skin microbiota of five pelagic fish species from the Atlantic Ocean. Int Microbiol 2024:10.1007/s10123-024-00524-8. [PMID: 38740652 DOI: 10.1007/s10123-024-00524-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/25/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024]
Abstract
The gills and skin microbiota and microbiome of wild fish remain far more under-investigated compared to that of farmed fish species, despite that these animal-microbe interactions hold the same ecophysiological roles in both cases. In this study, the gills and skin bacterial microbiota profiles and their presumptive bacterial metabolisms were investigated in five open-sea fishes: bullet tuna (Auxis sp.), common dolphinfish (Coryphaena hippurus), Atlantic little tunny (Euthynnus alletteratus), Atlantic bonito (Sarda sarda) and Atlantic white marlin (Kajikia albida). Gills and skin tissues were collected from two to three individuals per species, from specimens caught by recreational trolling during summer of 2019, and their bacterial 16S rRNA gene diversity was analysed by high-throughput sequencing. The gills bacterial communities among the five species were clearly different but not the skin bacterial microbiota. The dominant operational taxonomic units belonged to the Moraxellaceae, Pseudomonadaceae, Rhodobacteraceae, Staphylococcaceae and Vibrionaceae families. Despite the differences in taxonomic composition, the presumptive bacterial metabolisms between the gills and skin of the five fishes investigated here were ≥ 94% similar and were dominated by basic metabolism, most likely reflecting the continuous exposure of these tissues in the surrounding seawater.
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Affiliation(s)
- José Luis Varela
- Department of Biology, University of Cádiz, Puerto Real, 11510, Cádiz, Spain
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece
| | - Antonio Medina
- Department of Biology, University of Cádiz, Puerto Real, 11510, Cádiz, Spain
| | - Sokratis Papaspyrou
- Department of Biology, University of Cádiz, Puerto Real, 11510, Cádiz, Spain
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece.
- Agricultural Development Institute, University Research and Innovation Centre "IASON", Argonafton & Filellinon, 382 21, Volos, Greece.
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17
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Rehman A, Tian C, He S, Li H, Lu S, Du X, Peng Z. Transcriptome dynamics of Gossypium purpurascens in response to abiotic stresses by Iso-seq and RNA-seq data. Sci Data 2024; 11:477. [PMID: 38724643 PMCID: PMC11081948 DOI: 10.1038/s41597-024-03334-9] [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: 02/09/2024] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
Gossypium purpurascens is a member of the Malvaceae family, holds immense economic significance as a fiber crop worldwide. Abiotic stresses harm cotton crops, reduce yields, and cause economic losses. Generating high-quality reference genomes and large-scale transcriptomic datasets across diverse conditions can offer valuable insights into identifying preferred agronomic traits for crop breeding. The present research used leaf tissues to conduct PacBio Iso-seq and RNA-seq analysis. We carried out an in-depth analysis of DEGs using both correlations with cluster analysis and principal component analysis. Additionally, the study also involved the identification of both lncRNAs and CDS. We have prepared RNA-seq libraries from 75 RNA samples to study the effects of drought, salinity, alkali, and saline-alkali stress, as well as control conditions. A total of 454.06 Gigabytes of transcriptome data were effectively validated through the identification of differentially expressed genes and KEGG and GO analysis. Overwhelmingly, gene expression profiles and full-length transcripts from cotton tissues will aid in understanding the genetic mechanism of abiotic stress tolerance in G. purpurascens.
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Affiliation(s)
- Abdul Rehman
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Chunyan Tian
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Shoupu He
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, 455000, China
| | - Hongge Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, 455000, China
| | - Shuai Lu
- National Supercomputing Center in Zhengzhou, Zhengzhou University, Zhengzhou, 450001, China
| | - Xiongming Du
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, 455000, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, 572024, China.
| | - Zhen Peng
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, 455000, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, 572024, China.
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18
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Kirsch JM, Hryckowian AJ, Duerkop BA. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. Cell Host Microbe 2024; 32:739-754.e4. [PMID: 38565143 PMCID: PMC11081829 DOI: 10.1016/j.chom.2024.03.005] [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: 10/16/2023] [Revised: 02/06/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to the insertion of "hot spots" in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota, and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain-level variation within the microbiota impacts human health.
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Affiliation(s)
- Joshua M Kirsch
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045, USA
| | - Andrew J Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA; Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045, USA.
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19
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Khan MM, Sidorczuk K, Becker J, Aleksandrowicz A, Baraniewicz K, Ludwig C, Ali A, Kingsley RA, Schierack P, Kolenda R. Characterization of clumpy adhesion of Escherichia coli to human cells and associated factors influencing antibiotic sensitivity. Microbiol Spectr 2024; 12:e0260623. [PMID: 38530058 PMCID: PMC11064533 DOI: 10.1128/spectrum.02606-23] [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: 06/24/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024] Open
Abstract
Escherichia coli intestinal infection pathotypes are characterized by distinct adhesion patterns, including the recently described clumpy adhesion phenotype. Here, we identify and characterize the genetic factors contributing to the clumpy adhesion of E. coli strain 4972. In this strain, the transcriptome and proteome of adhered bacteria were found to be distinct from planktonic bacteria in the supernatant. A total of 622 genes in the transcriptome were differentially expressed in bacteria present in clumps relative to the planktonic bacteria. Seven genes targeted for disruption had variable distribution in different pathotypes and nonpathogenic E. coli, with the pilV and spnT genes being the least frequent or absent from most groups. Deletion (Δ) of five differentially expressed genes, flgH, ffp, pilV, spnT, and yggT, affected motility, adhesion, or antibiotic stress. ΔflgH exhibited 80% decrease and ΔyggT depicted 184% increase in adhesion, and upon complementation, adhesion was significantly reduced to 13%. ΔflgH lost motility and was regenerated when complemented, whereas Δffp had significantly increased motility, and reintroduction of the same gene reduced it to the wild-type level. The clumps produced by Δffp and ΔspnT were more resistant and protected the bacteria, with ΔspnT showing the best clump formation in terms of ampicillin stress protection. ΔyggT had the lowest tolerance to gentamicin, where the antibiotic stress completely eliminated the bacteria. Overall, we were able to investigate the influence of clump formation on cell surface adhesion and antimicrobial tolerance, with the contribution of several factors crucial to clump formation on susceptibility to the selected antibiotics. IMPORTANCE The study explores a biofilm-like clumpy adhesion phenotype in Escherichia coli, along with various factors and implications for antibiotic susceptibility. The phenotype permitted the bacteria to survive the onslaught of high antibiotic concentrations. Profiles of the transcriptome and proteome allowed the differentiation between adhered bacteria in clumps and planktonic bacteria in the supernatant. The deletion mutants of genes differentially expressed between adhered and planktonic bacteria, i.e., flgH, ffp, pilV, spnT, and yggT, and respective complementations in trans cemented their roles in multiple capacities. ffp, an uncharacterized gene, is involved in motility and resistance to ampicillin in a clumpy state. The work also affirms for the first time the role of the yggT gene in adhesion and its involvement in susceptibility against another aminoglycoside antibiotic, i.e., gentamicin. Overall, the study contributes to the mechanisms of biofilm-like adhesion phenotype and understanding of the antimicrobial therapy failures and infections of E. coli.
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Affiliation(s)
- Muhammad Moman Khan
- Institute for Biotechnology, Brandenburg University of Technology (BTU) Cottbus-Senftenberg, Senftenberg, Germany
| | - Katarzyna Sidorczuk
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Juliane Becker
- Institute for Biotechnology, Brandenburg University of Technology (BTU) Cottbus-Senftenberg, Senftenberg, Germany
| | - Adrianna Aleksandrowicz
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Karolina Baraniewicz
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wrocław, Wrocław, Poland
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences, Technical University Munich (TUM), Munich, Germany
| | - Aamir Ali
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Robert A. Kingsley
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Peter Schierack
- Institute for Biotechnology, Brandenburg University of Technology (BTU) Cottbus-Senftenberg, Senftenberg, Germany
| | - Rafał Kolenda
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
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20
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Nebauer DJ, Pearson LA, Neilan BA. Critical steps in an environmental metaproteomics workflow. Environ Microbiol 2024; 26:e16637. [PMID: 38760994 DOI: 10.1111/1462-2920.16637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/30/2024] [Indexed: 05/20/2024]
Abstract
Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As the field is still maturing, it lacks consistent workflows, making it challenging for non-expert researchers to navigate. This review aims to introduce the workflow of environmental metaproteomics. It outlines the standard practices for sample collection, processing, and analysis, and offers strategies to overcome the unique challenges presented by common environmental matrices such as soil, freshwater, marine environments, biofilms, sludge, and symbionts. The review also highlights the bottlenecks in data analysis that are specific to metaproteomics samples and provides suggestions for researchers to obtain high-quality datasets. It includes recent benchmarking studies and descriptions of software packages specifically built for metaproteomics analysis. The article is written without assuming the reader's familiarity with single-organism proteomic workflows, making it accessible to those new to proteomics or mass spectrometry in general. This primer for environmental metaproteomics aims to improve accessibility to this exciting technology and empower researchers to tackle challenging and ambitious research questions. While it is primarily a resource for those new to the field, it should also be useful for established researchers looking to streamline or troubleshoot their metaproteomics experiments.
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Affiliation(s)
- Daniel J Nebauer
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia
- Centre of Excellence in Synthetic Biology, Australian Research Council, Sydney, New South Wales, Australia
| | - Leanne A Pearson
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia
- Centre of Excellence in Synthetic Biology, Australian Research Council, Sydney, New South Wales, Australia
| | - Brett A Neilan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia
- Centre of Excellence in Synthetic Biology, Australian Research Council, Sydney, New South Wales, Australia
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21
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Wei J, Luo J, Peng T, Zhou P, Zhang J, Yang F. Comparative genomic analysis and functional investigations for MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria in ecology. ENVIRONMENTAL RESEARCH 2024; 248:118336. [PMID: 38295970 DOI: 10.1016/j.envres.2024.118336] [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: 08/21/2023] [Revised: 01/06/2024] [Accepted: 01/27/2024] [Indexed: 02/07/2024]
Abstract
Microcystins (MCs) significantly threaten the ecosystem and public health. Biodegradation has emerged as a promising technology for removing MCs. Many MCs-degrading bacteria have been identified, including an indigenous bacterium Sphingopyxis sp. YF1 that could degrade MC-LR and Adda completely. Herein, we gained insight into the MCs biodegradation mechanisms and evolutionary dynamics of MCs-degrading bacteria, and revealed the toxic risks of the MCs degradation products. The biochemical characteristics and genetic repertoires of strain YF1 were explored. A comparative genomic analysis was performed on strain YF1 and six other MCs-degrading bacteria to investigate their functions. The degradation products were investigated, and the toxicity of the intermediates was analyzed through rigorous theoretical calculation. Strain YF1 might be a novel species that exhibited versatile substrate utilization capabilities. Many common genes and metabolic pathways were identified, shedding light on shared functions and catabolism in the MCs-degrading bacteria. The crucial genes involved in MCs catabolism mechanisms, including mlr and paa gene clusters, were identified successfully. These functional genes might experience horizontal gene transfer events, suggesting the evolutionary dynamics of these MCs-degrading bacteria in ecology. Moreover, the degradation products for MCs and Adda were summarized, and we found most of the intermediates exhibited lower toxicity to different organisms than the parent compound. These findings systematically revealed the MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria. Consequently, this research contributed to the advancement of green biodegradation technology in aquatic ecology, which might protect human health from MCs.
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Affiliation(s)
- Jia Wei
- Xiangya School of Public Health, Central South University, Changsha, Hunan, 410078, China
| | - Jiayou Luo
- Xiangya School of Public Health, Central South University, Changsha, Hunan, 410078, China.
| | - Tangjian Peng
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang, Hunan, 421001, China
| | - Pengji Zhou
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang, Hunan, 421001, China
| | - Jiajia Zhang
- Xiangya School of Public Health, Central South University, Changsha, Hunan, 410078, China
| | - Fei Yang
- Xiangya School of Public Health, Central South University, Changsha, Hunan, 410078, China; Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang, Hunan, 421001, China.
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22
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Li Z, Geng G, Xie H, Zhou L, Wang L, Qiao F. Metabolomic and transcriptomic reveal flavonoid biosynthesis and regulation mechanism in Phlomoides rotata from different habitats. Genomics 2024; 116:110850. [PMID: 38685286 DOI: 10.1016/j.ygeno.2024.110850] [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: 02/24/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
Phlomoides rotata is a traditional medical plant at 3100-5200 m altitude in the Tibet Plateau. In this study, flavonoid metabolites were investigated in P. rotata from Henan County (HN), Guoluo County (GL), Yushu County (YS), and Chengduo County (CD) habitats in Qinghai. The level of kaempferol 3-neohesperidoside, sakuranetin, and biochanin A was high in HN. The content of limocitrin and isoquercetin was high in YS. The levels of ikarisoside A and chrysosplenol D in GL were high. Schaftoside, miquelianin, malvidin chloride, and glabrene in CD exhibited high levels. The results showed a significant correlation between 59 flavonoids and 29 DEGs. Eleven flavonoids increased with altitude. PAL2, UFGT6, COMT1, HCT2, 4CL4, and HCT3 genes were crucial in regulating flavonoid biosynthesis. Three enzymes CHS, 4CL, and UFGT, were crucial in regulating flavonoid biosynthesis. This study provided biological and chemical evidence for the different uses of various regional plants of P. rotata.
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Affiliation(s)
- Zuxia Li
- Key Laboratory of Tibetan Plateau Medicinal Plant and Animal Resources, School of Life Sciences, Qinghai Normal University, Xining 810008, China
| | - Guigong Geng
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
| | - Huichun Xie
- Key Laboratory of Tibetan Plateau Medicinal Plant and Animal Resources, School of Life Sciences, Qinghai Normal University, Xining 810008, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
| | - Lianyu Zhou
- Key Laboratory of Tibetan Plateau Medicinal Plant and Animal Resources, School of Life Sciences, Qinghai Normal University, Xining 810008, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
| | - Luhao Wang
- Key Laboratory of Tibetan Plateau Medicinal Plant and Animal Resources, School of Life Sciences, Qinghai Normal University, Xining 810008, China
| | - Feng Qiao
- Key Laboratory of Tibetan Plateau Medicinal Plant and Animal Resources, School of Life Sciences, Qinghai Normal University, Xining 810008, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China.
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Meng XJ, Wang LQ, Ma BG, Wei XH, Zhou Y, Sun ZX, Li YY. Screening, identification and evaluation of an acidophilic strain of Bacillus velezensis B4-7 for the biocontrol of tobacco bacterial wilt. FRONTIERS IN PLANT SCIENCE 2024; 15:1360173. [PMID: 38751839 PMCID: PMC11094357 DOI: 10.3389/fpls.2024.1360173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/15/2024] [Indexed: 05/18/2024]
Abstract
Tobacco (Nicotiana tabacum L.) bacterial wilt, caused by Ralstonia solanacearum, is indeed a highly destructive plant disease, leading to substantial damage in tobacco production. While biological control is considered an effective measure for managing bacterial wilt, related research in this area has been relatively limited compared to other control methods. In order to discover new potential antagonistic bacteria with high biocontrol efficacy against tobacco bacterial wilt, we conducted an analysis of the microbial composition differences between disease-suppressive and disease-conducive soils using Illumina sequencing. As a result, we successfully isolated six strains from the disease-suppressive soil that exhibited antibacterial activity against Ralstonia solanacearum. Among these strains, B4-7 showed the strongest antibacterial activity, even at acidic conditions with a pH of 4.0. Based on genome analysis using Average Nucleotide Identity (ANI), B4-7 was identified as Bacillus velezensis. In greenhouse and field trials, strain B4-7 significantly reduced the disease index of tobacco bacterial wilt, with control efficiencies reaching 74.03% and 46.88% respectively. Additionally, B4-7 exhibited plant-promoting abilities that led to a 35.27% increase in tobacco production in field conditions. Quantitative real-time (qPCR) analysis demonstrated that strain B4-7 effectively reduced the abundance of R. solanacearum in the rhizosphere. Genome sequencing and Liquid Chromatography-Mass Spectrometry (LC-MS) analysis revealed that strain B4-7 potentially produces various lipopeptide metabolites, such as microlactin, bacillaene, difficidin, bacilysin, and surfactin. Furthermore, B4-7 influenced the structure of the rhizosphere soil microbial community, increasing bacterial abundance and fungal diversity, while also promoting the growth of different beneficial microorganisms. In addition, B4-7 enhanced tobacco's resistance to R. solanacearum by increasing the activities of defense enzymes, including superoxide dismutase (SOD), phenylalanine ammonia-lyase (PAL), peroxidase (POD), catalase (CAT), and polyphenol oxidase (PPO). Collectively, these findings suggest that B. velezensis B4-7 holds significant biocontrol potential and can be considered a promising candidate strain for eco-friendly management of tobacco bacterial wilt.
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Affiliation(s)
- Xiang-jia Meng
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Lan-qin Wang
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Bai-ge Ma
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Xi-hong Wei
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Yi Zhou
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
- Early Detection and Management of Agricultural and Forestry Pests, Jingzhou, Hubei, China
| | - Zheng-xiang Sun
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
- Early Detection and Management of Agricultural and Forestry Pests, Jingzhou, Hubei, China
| | - Yan-yan Li
- Tobacco Research Institute of Hubei Province, Wuhan, Hubei, China
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24
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Balasco N, Damaggio G, Esposito L, Colonna V, Vitagliano L. A comprehensive analysis of SARS-CoV-2 missense mutations indicates that all possible amino acid replacements in the viral proteins occurred within the first two-and-a-half years of the pandemic. Int J Biol Macromol 2024; 266:131054. [PMID: 38522702 DOI: 10.1016/j.ijbiomac.2024.131054] [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: 01/25/2024] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
The surveillance of COVID-19 pandemic has led to the determination of millions of genome sequences of the SARS-CoV-2 virus, with the accumulation of a wealth of information never collected before for an infectious disease. Exploring the information retrieved from the GISAID database reporting at that time >13 million genome sequences, we classified the 141,639 unique missense mutations detected in the first two-and-a-half years (up to October 2022) of the pandemic. Notably, our analysis indicates that 98.2 % of all possible conservative amino acid replacements occurred. Even non-conservative mutations were highly represented (73.9 %). For a significant number of residues (3 %), all possible replacements with the other nineteen amino acids have been observed. These observations strongly indicate that, in this time interval, the virus explored all possible alternatives in terms of missense mutations for all sites of its polypeptide chain and that those that are not observed severely affect SARS-CoV-2 integrity. The implications of the present findings go well beyond the structural biology of SARS-CoV-2 as the huge amount of information here collected and classified may be valuable for the elucidation of the sequence-structure-function relationships in proteins.
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Affiliation(s)
- Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Dep. Chemistry, Sapienza University of Rome, Rome, Italy.
| | - Gianluca Damaggio
- Institute of Genetics and Biophysics, CNR, Naples, Italy; Laboratory of Stem Cell Biology and Pharmacology of Neurodegenerative Diseases, Department of Biosciences, University of Milan, Milan, Italy; University of Naples Federico II, Naples, Italy
| | | | - Vincenza Colonna
- Institute of Genetics and Biophysics, CNR, Naples, Italy; Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
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25
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Cuan R, Liu S, Zhou C, Wang S, Zheng Y, Yuan Y. Transcriptome Analysis of mfs2-Defective Penicillium digitatum Mutant to Reveal Importance of Pd mfs2 in Developing Fungal Prochloraz Resistance. Microorganisms 2024; 12:888. [PMID: 38792718 PMCID: PMC11123787 DOI: 10.3390/microorganisms12050888] [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: 03/20/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Demethylation inhibitors (DMIs), including prochloraz, are popular fungicides to control citrus postharvest pathogens such as Penicillium digitatum (green mold). However, many P. digitatum strains have developed prochloraz resistance, which decreases drug efficacy. Specific major facilitator superfamily (MFS) transporter gene mfs2, encoding drug-efflux pump protein MFS2, has been identified in P. digitatum strain F6 (PdF6) to confer fungal strain prochloraz resistance. However, except for the drug-efflux pump function of MFS2, other mechanisms relating to the Pdmfs2 are not fully clear. The present study reported a transcriptome investigation on the mfs2-defective P. digitatum strain. Comparing to the wild-type strain, the mfs2-defective strain showed 717 differentially expressed genes (DEGs) without prochloraz induction, and 1221 DEGs with prochloraz induction. The obtained DEGs included multiple isoforms of MFS transporter-encoding genes, ATP-binding cassette (ABC) transporter-encoding genes, and multidrug and toxic compound extrusion (MATE) family protein-encoding genes. Many of these putative drug-efflux pump protein-encoding genes had significantly lower transcript abundances in the mfs2-defective P. digitatum strain at prochloraz induction, as compared to the wild-type strain, including twenty-two MFS transporter-encoding genes (MFS1 to MFS22), two ABC transporter-encoding genes (ABC1 and ABC2), and three MATE protein-encoding genes (MATE1 to MATE3). The prochloraz induction on special drug-efflux pump protein genes in the wild-type strain was not observed in the mfs2-defective strain, including MFS21, MFS22, ABC2, MATE1, MATE2, and MATE3. On the other hand, the up-regulation of other drug-efflux pump protein genes in the mfs2-defective strain cannot recover the fungal prochloraz resistance, including MFS23, MFS26, MFS27, MFS31, MFS33, and ABC3 to ABC8. The functional enrichment of DEGs based on Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and euKaryotic Orthologous Groups (KOG) database resources suggested some essential contributors to the mfs2-relating prochloraz resistance, including ribosome biosynthesis-related genes, oxidative phosphorylation genes, steroid biosynthesis-related genes, fatty acid and lipid metabolism-related genes, and carbon- and nitrogen-metabolism-related genes. The results indicated that the MFS2 transporter might be involved in the regulation of multiple drug-efflux pump protein gene expressions and multiple metabolism-related gene expressions, thus playing an important role in developing P. digitatum prochloraz resistance.
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Affiliation(s)
- Rongrong Cuan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China; (R.C.); (C.Z.); (S.W.)
| | - Shaoting Liu
- School of Political and Law, Huanggang Normal University, Huanggang 438000, China;
| | - Chuanyou Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China; (R.C.); (C.Z.); (S.W.)
| | - Shengqiang Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China; (R.C.); (C.Z.); (S.W.)
| | - Yongliang Zheng
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization & Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang 438000, China;
| | - Yongze Yuan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China; (R.C.); (C.Z.); (S.W.)
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26
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Niu J, Zhao J, Guo Q, Zhang H, Yue A, Zhao J, Yin C, Wang M, Du W. WGCNA Reveals Hub Genes and Key Gene Regulatory Pathways of the Response of Soybean to Infection by Soybean mosaic virus. Genes (Basel) 2024; 15:566. [PMID: 38790195 PMCID: PMC11120672 DOI: 10.3390/genes15050566] [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: 03/27/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Soybean mosaic virus (SMV) is one of the main pathogens that can negatively affect soybean production and quality. To study the gene regulatory network of soybeans in response to SMV SC15, the resistant line X149 and susceptible line X97 were subjected to transcriptome analysis at 0, 2, 8, 12, 24, and 48 h post-inoculation (hpi). Differential expression analysis revealed that 10,190 differentially expressed genes (DEGs) responded to SC15 infection. Weighted gene co-expression network analysis (WGCNA) was performed to identify highly related resistance gene modules; in total, eight modules, including 2256 DEGs, were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of 2256 DEGs revealed that the genes significantly clustered into resistance-related pathways, such as the plant-pathogen interaction pathway, mitogen-activated protein kinases (MAPK) signaling pathway, and plant hormone signal transduction pathway. Among these pathways, we found that the flg22, Ca2+, hydrogen peroxide (H2O2), and abscisic acid (ABA) regulatory pathways were fully covered by 36 DEGs. Among the 36 DEGs, the gene Glyma.01G225100 (protein phosphatase 2C, PP2C) in the ABA regulatory pathway, the gene Glyma.16G031900 (WRKY transcription factor 22, WRKY22) in Ca2+ and H2O2 regulatory pathways, and the gene Glyma.04G175300 (calcium-dependent protein kinase, CDPK) in Ca2+ regulatory pathways were highly connected hub genes. These results indicate that the resistance of X149 to SC15 may depend on the positive regulation of flg22, Ca2+, H2O2, and ABA regulatory pathways. Our study further showed that superoxide dismutase (SOD) activity, H2O2 content, and catalase (CAT) and peroxidase (POD) activities were significantly up-regulated in the resistant line X149 compared with those in 0 hpi. This finding indicates that the H2O2 regulatory pathway might be dependent on flg22- and Ca2+-pathway-induced ROS generation. In addition, two hub genes, Glyma.07G190100 (encoding F-box protein) and Glyma.12G185400 (encoding calmodulin-like proteins, CMLs), were also identified and they could positively regulate X149 resistance. This study provides pathways for further investigation of SMV resistance mechanisms in soybean.
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Affiliation(s)
- Jingping Niu
- College of Life Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, China;
| | - Jing Zhao
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| | - Qian Guo
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| | - Hanyue Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| | - Aiqin Yue
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| | - Jinzhong Zhao
- Department of Basic Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (C.Y.)
| | - Congcong Yin
- Department of Basic Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (C.Y.)
| | - Min Wang
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| | - Weijun Du
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
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Choudhary G, Kumari S, Anu K, Devi S. Deciphering the microbial communities of alkaline hot spring in Panamik, Ladakh, India using a high-throughput sequencing approach. Braz J Microbiol 2024:10.1007/s42770-024-01346-6. [PMID: 38662153 DOI: 10.1007/s42770-024-01346-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Due to their distinctive physicochemical characteristics, hot springs are extremely important. The whole genome metagenomic sequencing technology can be utilized to analyze the diverse microbial community that thrives in this habitat due to the particular selection pressure that prevails there. The current investigation emphasizes on culture-independent metagenomic study of the Panamik hot spring and its nearby areas from Ladakh, India. Based on different diversity indices, sequence analysis of the soil reservoir showed higher species richness and diversity in comparison to water and sediment samples. The mineral content and various physicochemical pameters like temperature, pH had an impact on the composition of the microbial community of the geothermal springs. The phyla Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacter, Firmicutes, and Verrucomicrobia in bacterial domain dominate the thermos-alkaline spring at Panamik in different concentrations. Economically significant microbes from the genera Actinobacter, Thermosynechoccus, Candidatus Solibacter, Chthoniobacter, Synechoccus, Pseudomonas and Sphingomonas, were prevalent in hot spring. In the archaeal domain, the most dominant phylum and genera were Euryarchaeota and Thermococcus in all the samples. Further, the most abundant species were Methanosarcina barkeri, Nitrospumilus maritimus and Methanosarcina acetivorans. The present study which only examined one of the several thermal springs present in the Himalayan geothermal area, should be regarded as a preliminary investigation of the microbiota that live in the hot springs on these remote areas. These findings suggest that further investigations should be undertaken to characterize the ecosystems of the Panamik hot spring, which serve as a repository for unidentified microbial lineages.
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Affiliation(s)
- Geetanjli Choudhary
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Shalini Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Kumari Anu
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sarita Devi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Pan X, Liu H, Feng L, Zong Y, Cao Z, Guo L, Yang G. Full-length transcriptome analysis of a bloom-forming dinoflagellate Prorocentrum shikokuense (Dinophyceae). Sci Data 2024; 11:430. [PMID: 38664437 PMCID: PMC11045741 DOI: 10.1038/s41597-024-03269-1] [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: 02/23/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Prorocentrum shikokuense (formerly P. donghaiense) is a pivotal dinoflagellate species associating with the HABs in the East China Sea. The complexity of its large nuclear genome hindered us from understanding its genomic characteristics. Full-length transcriptome sequencing offers a practical solution to decipher the physiological mechanisms of a species without the reference genome. In this study, we employed single-molecule real-time (SMRT) sequencing technology to sequence the full-length transcriptome of Prorocentrum shikokuense. We successfully generated 41.73 Gb of clean SMRT sequencing reads and isolated 105,249 non-redundant full-length non-chimeric reads. Our trial has led to the identification of 11,917 long non-coding RNA transcripts, 514 alternative splicing events, 437 putative transcription factor genes from 17 TF gene families, and 34,723 simple sequence repeats. Additionally, a total of 78,265 open reading frames were identified, of them 15,501 were the protein coding sequences. This dataset is valuable for annotating P. shikokuense genome, and will contribute significantly to the in-depth studies on the molecular mechanisms underlining the dinoflagellate bloom formation.
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Affiliation(s)
- Xiaohui Pan
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, P. R. China
| | - Hang Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, P. R. China
| | - Leili Feng
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, P. R. China
| | - Yanan Zong
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, P. R. China
| | - Zihao Cao
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, P. R. China
| | - Li Guo
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, P. R. China.
| | - Guanpin Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, P. R. China.
- Key Laboratory of Evolution and Marine Biodiversity of Ministry of Education, Ocean University of China (OUC), Qingdao, 266003, P. R. China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, P. R. China.
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Lu K, Wang X, Zhou Y, Zhu Q. Genomic characterization and probiotic potential assessment of an exopolysaccharide-producing strain Pediococcus pentosaceus LL-07 isolated from fermented meat. BMC Microbiol 2024; 24:142. [PMID: 38664612 PMCID: PMC11044368 DOI: 10.1186/s12866-024-03304-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND The genomic information available for Pediococcus pentosaceus is primarily derived from fermented fruits and vegetables, with less information available from fermented meat. P. pentosaceus LL-07, a strain isolated from fermented meat, has the capability of producing exopolysaccharides (EPS). To assess the probiotic attributes of P. pentosaceus LL-07, we conducted whole-genome sequencing (WGS) using the PacBio SequelIIe and Illumina MiSeq platforms, followed by in vitro experiments to explore its probiotic potential. RESULTS The genome size of P. pentosaceus LL-07 is 1,782,685 bp, comprising a circular chromosome and a circular plasmid. Our investigation revealed the absence of a CRISPR/Cas system. Sugar fermentation experiments demonstrated the characteristics of carbohydrate metabolism. P. pentosaceus LL-07 contains an EPS synthesis gene cluster consisting of 13 genes, which is different from the currently known gene cluster structure. NO genes associated with hemolysis or toxin synthesis were detected. Additionally, eighty-six genes related to antibiotic resistance were identified but not present in the prophage, transposon or plasmid. In vitro experiments demonstrated that P. pentosaceus LL-07 was comparable to the reference strain P. pentosaceus ATCC25745 in terms of tolerance to artificial digestive juice and bile, autoaggregation and antioxidation, and provided corresponding genomic evidence. CONCLUSION This study confirmed the safety and probiotic properties of P. pentosaceus LL-07 via complete genome and phenotype analysis, supporting its characterization as a potential probiotic candidate.
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Affiliation(s)
- Kuan Lu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guizhou Province, Guiyang, 550025, China
- Guizhou Province Key Laboratory of Agricultural and Animal Products Storage and Processing, School of Liquor and Food Engineering, Guizhou University, Guizhou, Guiyang, 550025, China
| | - Xueya Wang
- Chili Pepper Research Institute, Guizhou Provincial Academy of Agricultural Sciences, Guizhou, Guiyang, 550006, China
| | - Ying Zhou
- Guizhou Province Key Laboratory of Agricultural and Animal Products Storage and Processing, School of Liquor and Food Engineering, Guizhou University, Guizhou, Guiyang, 550025, China
| | - Qiujin Zhu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guizhou Province, Guiyang, 550025, China.
- Guizhou Province Key Laboratory of Agricultural and Animal Products Storage and Processing, School of Liquor and Food Engineering, Guizhou University, Guizhou, Guiyang, 550025, China.
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30
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Zhu J, Wang X, Zhao J, Ji F, Zeng J, Wei Y, Xu L, Dong G, Ma X, Wang C. Genomic characterization and related functional genes of γ- poly glutamic acid producing Bacillus subtilis. BMC Microbiol 2024; 24:125. [PMID: 38622505 PMCID: PMC11017564 DOI: 10.1186/s12866-024-03262-z] [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: 11/04/2023] [Accepted: 03/15/2024] [Indexed: 04/17/2024] Open
Abstract
γ- poly glutamic acid (γ-PGA), a high molecular weight polymer, is synthesized by microorganisms and secreted into the extracellular space. Due to its excellent performance, γ-PGA has been widely used in various fields, including food, biomedical and environmental fields. In this study, we screened natto samples for two strains of Bacillus subtilis N3378-2at and N3378-3At that produce γ-PGA. We then identified the γ-PGA synthetase gene cluster (PgsB, PgsC, PgsA, YwtC and PgdS), glutamate racemase RacE, phage-derived γ-PGA hydrolase (PghB and PghC) and exo-γ-glutamyl peptidase (GGT) from the genome of these strains. Based on these γ-PGA-related protein sequences from isolated Bacillus subtilis and 181 B. subtilis obtained from GenBank, we carried out genotyping analysis and classified them into types 1-5. Since we found B. amyloliquefaciens LL3 can produce γ-PGA, we obtained the B. velezensis and B. amyloliquefaciens strains from GenBank and classified them into types 6 and 7 based on LL3. Finally, we constructed evolutionary trees for these protein sequences. This study analyzed the distribution of γ-PGA-related protein sequences in the genomes of B. subtilis, B. velezensis and B. amyloliquefaciens strains, then the evolutionary diversity of these protein sequences was analyzed, which provided novel information for the development and utilization of γ-PGA-producing strains.
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Affiliation(s)
- Jiayue Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xue Wang
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Jianan Zhao
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Fang Ji
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Jun Zeng
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Yanwen Wei
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - LiLi Xu
- Union Biology (Shanghai) Co., Ltd, Shanghai, 201100, China
| | - Guoying Dong
- College of Global Change and Earth System Science, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Xingyuan Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Chengmin Wang
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China.
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Deng L, Wang Q, Liu H, Jiang Y, Xu M, Xiang Y, Yang T, Yang S, Yan D, Li M, Zhao L, Zhao X, Wan K, He G, Mijiti X, Li G. Identification of positively selected genes in Mycobacterium tuberculosis from southern Xinjiang Uygur autonomous region of China. Front Microbiol 2024; 15:1290227. [PMID: 38686109 PMCID: PMC11056549 DOI: 10.3389/fmicb.2024.1290227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
Background Tuberculosis (TB), mainly caused by Mycobacterium tuberculosis (Mtb), remains a serious public health problem. Increasing evidence supports that selective evolution is an important force affecting genomic determinants of Mtb phenotypes. It is necessary to further understand the Mtb selective evolution and identify the positively selected genes that probably drive the phenotype of Mtb. Methods This study mainly focused on the positive selection of 807 Mtb strains from Southern Xinjiang of China using whole genome sequencing (WGS). PAML software was used for identifying the genes and sites under positive selection in 807 Mtb strains. Results Lineage 2 (62.70%) strains were the dominant strains in this area, followed by lineage 3 (19.45%) and lineage 4 (17.84%) strains. There were 239 codons in 47 genes under positive selection, and the genes were majorly associated with the functions of transcription, defense mechanisms, and cell wall/membrane/envelope biogenesis. There were 28 codons (43 mutations) in eight genes (gyrA, rpoB, rpoC, katG, pncA, embB, gid, and cut1) under positive selection in multi-drug resistance (MDR) strains but not in drug-susceptible (DS) strains, in which 27 mutations were drug-resistant loci, 9 mutations were non-drug-resistant loci but were in drug-resistant genes, 2 mutations were compensatory mutations, and 5 mutations were in unknown drug-resistant gene of cut1. There was a codon in Rv0336 under positive selection in L3 strains but not in L2 and L4 strains. The epitopes of T and B cells were both hyper-conserved, particularly in the T-cell epitopes. Conclusion This study revealed the ongoing selective evolution of Mtb. We found some special genes and sites under positive selection which may contribute to the advantage of MDR and L3 strains. It is necessary to further study these mutations to understand their impact on phenotypes for providing more useful information to develop new TB interventions.
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Affiliation(s)
- Lele Deng
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Quan Wang
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Haican Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Jiang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Miao Xu
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yu Xiang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, University of South China, Hengyang, China
| | - Ting Yang
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Shuliu Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, University of South China, Hengyang, China
| | - Di Yan
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Machao Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lili Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiuqin Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kanglin Wan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guangxue He
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaokaiti Mijiti
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Guilian Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Bao Y, Zhang Q, Huang J, Zhang S, Yao W, Yu Z, Deng Z, Yu J, Kong W, Yu X, Lu S, Wang Y, Li R, Song Y, Zou C, Xu Y, Liu Z, Yu F, Song J, Huang Y, Zhang J, Wang H, Chen B, Zhang X, Zhang M. A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution. Nat Commun 2024; 15:3041. [PMID: 38589412 PMCID: PMC11001919 DOI: 10.1038/s41467-024-47390-6] [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: 10/05/2023] [Accepted: 03/31/2024] [Indexed: 04/10/2024] Open
Abstract
Sugarcane is a vital crop with significant economic and industrial value. However, the cultivated sugarcane's ultra-complex genome still needs to be resolved due to its high ploidy and extensive recombination between the two subgenomes. Here, we generate a chromosomal-scale, haplotype-resolved genome assembly for a hybrid sugarcane cultivar ZZ1. This assembly contains 10.4 Gb genomic sequences and 68,509 annotated genes with defined alleles in two sub-genomes distributed in 99 original and 15 recombined chromosomes. RNA-seq data analysis shows that sugar accumulation-associated gene families have been primarily expanded from the ZZSO subgenome. However, genes responding to pokkah boeng disease susceptibility have been derived dominantly from the ZZSS subgenome. The region harboring the possible smut resistance genes has expanded significantly. Among them, the expansion of WAK and FLS2 families is proposed to have occurred during the breeding of ZZ1. Our findings provide insights into the complex genome of hybrid sugarcane cultivars and pave the way for future genomics and molecular breeding studies in sugarcane.
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Affiliation(s)
- Yixue Bao
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Qing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Jiangfeng Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Shengcheng Zhang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Zehuai Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Zuhu Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Jiaxin Yu
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Weilong Kong
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Xikai Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Shan Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Yibin Wang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Ru Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Yuhan Song
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Chengwu Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Yuzhi Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Zongling Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Fan Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Jiaming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Youzong Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Haifeng Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China.
| | - Xingtan Zhang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China.
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China.
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Giraud-Gatineau A, Ayachit G, Nieves C, Dagbo KC, Bourhy K, Pulido F, Huete SG, Benaroudj N, Picardeau M, Veyrier FJ. Inter-species Transcriptomic Analysis Reveals a Constitutive Adaptation Against Oxidative Stress for the Highly Virulent Leptospira Species. Mol Biol Evol 2024; 41:msae066. [PMID: 38573174 PMCID: PMC11021026 DOI: 10.1093/molbev/msae066] [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: 10/20/2023] [Revised: 02/29/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
Transcriptomic analyses across large scales of evolutionary distance have great potential to shed light on regulatory evolution but are complicated by difficulties in establishing orthology and limited availability of accessible software. We introduce here a method and a graphical user interface wrapper, called Annotator-RNAtor, for performing interspecies transcriptomic analysis and studying intragenus evolution. The pipeline uses third-party software to infer homologous genes in various species and highlight differences in the expression of the core-genes. To illustrate the methodology and demonstrate its usefulness, we focus on the emergence of the highly virulent Leptospira subclade known as P1+, which includes the causative agents of leptospirosis. Here, we expand on the genomic study through the comparison of transcriptomes between species from P1+ and their related P1- counterparts (low-virulent pathogens). In doing so, we shed light on differentially expressed pathways and focused on describing a specific example of adaptation based on a differential expression of PerRA-controlled genes. We showed that P1+ species exhibit higher expression of the katE gene, a well-known virulence determinant in pathogenic Leptospira species correlated with greater tolerance to peroxide. Switching PerRA alleles between P1+ and P1- species demonstrated that the lower repression of katE and greater tolerance to peroxide in P1+ species was solely controlled by PerRA and partly caused by a PerRA amino-acid permutation. Overall, these results demonstrate the strategic fit of the methodology and its ability to decipher adaptive transcriptomic changes, not observable by comparative genome analysis, that may have been implicated in the emergence of these pathogens.
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Affiliation(s)
- Alexandre Giraud-Gatineau
- Microbiology Department, Institut Pasteur, Université Paris Cité, Biology of Spirochetes Unit, Paris, France
| | - Garima Ayachit
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada
| | - Cecilia Nieves
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada
| | - Kouessi C Dagbo
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada
| | - Konogan Bourhy
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada
| | - Francisco Pulido
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada
| | - Samuel G Huete
- Microbiology Department, Institut Pasteur, Université Paris Cité, Biology of Spirochetes Unit, Paris, France
| | - Nadia Benaroudj
- Microbiology Department, Institut Pasteur, Université Paris Cité, Biology of Spirochetes Unit, Paris, France
| | - Mathieu Picardeau
- Microbiology Department, Institut Pasteur, Université Paris Cité, Biology of Spirochetes Unit, Paris, France
| | - Frédéric J Veyrier
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada
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Ma J, Gao R, Xie Q, Pan X, Tong N. Whole transcriptome sequencing analyses of islets reveal ncRNA regulatory networks underlying impaired insulin secretion and increased β-cell mass in high fat diet-induced diabetes mellitus. PLoS One 2024; 19:e0300965. [PMID: 38557554 PMCID: PMC10984535 DOI: 10.1371/journal.pone.0300965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
AIM Our study aims to identify novel non-coding RNA-mRNA regulatory networks associated with β-cell dysfunction and compensatory responses in obesity-related diabetes. METHODS Glucose metabolism, islet architecture and secretion, and insulin sensitivity were characterized in C57BL/6J mice fed on a 60% high-fat diet (HFD) or control for 24 weeks. Islets were isolated for whole transcriptome sequencing to identify differentially expressed (DE) mRNAs, miRNAs, IncRNAs, and circRNAs. Regulatory networks involving miRNA-mRNA, lncRNA-mRNA, and lncRNA-miRNA-mRNA were constructed and functions were assessed through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. RESULTS Despite compensatory hyperinsulinemia and a significant increase in β-cell mass with a slow rate of proliferation, HFD mice exhibited impaired glucose tolerance. In isolated islets, insulin secretion in response to glucose and palmitic acid deteriorated after 24 weeks of HFD. Whole transcriptomic sequencing identified a total of 1324 DE mRNAs, 14 DE miRNAs, 179 DE lncRNAs, and 680 DE circRNAs. Our transcriptomic dataset unveiled several core regulatory axes involved in the impaired insulin secretion in HFD mice, such as miR-6948-5p/Cacna1c, miR-6964-3p/Cacna1b, miR-3572-5p/Hk2, miR-3572-5p/Cckar and miR-677-5p/Camk2d. Additionally, proliferative and apoptotic targets, including miR-216a-3p/FKBP5, miR-670-3p/Foxo3, miR-677-5p/RIPK1, miR-802-3p/Smad2 and ENSMUST00000176781/Caspase9 possibly contribute to the increased β-cell mass in HFD islets. Furthermore, competing endogenous RNAs (ceRNA) regulatory network involving 7 DE miRNAs, 15 DE lncRNAs and 38 DE mRNAs might also participate in the development of HFD-induced diabetes. CONCLUSIONS The comprehensive whole transcriptomic sequencing revealed novel non-coding RNA-mRNA regulatory networks associated with impaired insulin secretion and increased β-cell mass in obesity-related diabetes.
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Affiliation(s)
- Jinfang Ma
- Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu, China
- Center for Diabetes and Metabolism Research, West China Hospital, Sichuan University, Chengdu, China
| | - Rui Gao
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Qingxing Xie
- Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu, China
- Center for Diabetes and Metabolism Research, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaohui Pan
- Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu, China
- Center for Diabetes and Metabolism Research, West China Hospital, Sichuan University, Chengdu, China
| | - Nanwei Tong
- Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu, China
- Center for Diabetes and Metabolism Research, West China Hospital, Sichuan University, Chengdu, China
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Baker BA, Gutiérrez-Preciado A, Rodríguez Del Río Á, McCarthy CGP, López-García P, Huerta-Cepas J, Susko E, Roger AJ, Eme L, Moreira D. Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments. Nat Microbiol 2024; 9:964-975. [PMID: 38519541 DOI: 10.1038/s41564-024-01647-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/20/2024] [Indexed: 03/25/2024]
Abstract
Extremely halophilic archaea (Haloarchaea, Nanohaloarchaeota, Methanonatronarchaeia and Halarchaeoplasmatales) thrive in saturating salt concentrations where they must maintain osmotic equilibrium with their environment. The evolutionary history of adaptations enabling salt tolerance remains poorly understood, in particular because the phylogeny of several lineages is conflicting. Here we present a resolved phylogeny of extremely halophilic archaea obtained using improved taxon sampling and state-of-the-art phylogenetic approaches designed to cope with the strong compositional biases of their proteomes. We describe two uncultured lineages, Afararchaeaceae and Asbonarchaeaceae, which break the long branches at the base of Haloarchaea and Nanohaloarchaeota, respectively. We obtained 13 metagenome-assembled genomes (MAGs) of these archaea from metagenomes of hypersaline aquatic systems of the Danakil Depression (Ethiopia). Our phylogenomic analyses including these taxa show that at least four independent adaptations to extreme halophily occurred during archaeal evolution. Gene-tree/species-tree reconciliation suggests that gene duplication and horizontal gene transfer played an important role in this process, for example, by spreading key genes (such as those encoding potassium transporters) across extremely halophilic lineages.
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Affiliation(s)
- Brittany A Baker
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Ana Gutiérrez-Preciado
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Álvaro Rodríguez Del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Charley G P McCarthy
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Edward Susko
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew J Roger
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Laura Eme
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France.
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France.
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Hu P, Peng H, Man X, Xing Z, Wang C, Yu C, Xing J, Yan X, Zhang H, Zeng M, Bao L, Zou J, Zhu P, Xu Y. Transcriptomic analysis and oxidative stress induced by sodium dichloroisocyanurate in the intestine of Phascolosoma esculenta. Comp Biochem Physiol C Toxicol Pharmacol 2024; 278:109857. [PMID: 38354993 DOI: 10.1016/j.cbpc.2024.109857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/20/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024]
Abstract
Sodium dichloroisocyanurate (NaDCC, C3Cl2N3NaO3) is a solid chlorine-containing product that is widely used as a disinfectant in living environments, which has potential toxic effects on human and rats. Phascolosoma esculenta is a species native to the southeast coast of China and can be used as an indicator organism. In the present study, 150 P. esculenta were used to determine the LC50 of NaDCC for P. esculenta, then 100 P. esculenta were used to analysis the change of histopathology, oxidative stress and transcriptome after NaDCC exposure. The results showed that the LC50 of NaDCC for 48 h was 50 mg/L. NaDCC stress induced pathological events in P. esculenta, including blisters, intestinal structural damage and epithelial cell ruptured or even loss. The highest and lowest intestinal activity of superoxide dismutase in individual survivors was detected at 12 h and 72 h, respectively. Malondialdehyde levels in the intestine declined gradually from 3 h and increased at 9 h, and peaked at 12 h. Total antioxidant capacity declined at 3 h and dropped below the levels of control group after 9 h. Transcriptome sequencing analysis yielded a total of 48.65 Gb of clean data. A total of 34,759 new genes were found including 957 differentially expressed genes (DEGs). The DEGs were significantly enriched in ferroptosis, response to chemicals, response to stress, immune system, ion transport, cell death, oxidation-reduction, cellular homeostasis, protein ubiquitination, and protein neddylation. Additionally, the levels of detoxification enzymes, such as glutathione-S-transferase, cytochrome P450, ABC, UDP-glycosyltransferase and SLC transporters of endogenous and exogenous solutes were significantly changed. Overall, the results provide reference for reasonable use of disinfectants during farming, and also provide insight into the mechanisms related to NaDCC toxicity in P. esculenta.
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Affiliation(s)
- Peifen Hu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi 535011, China
| | - Huijing Peng
- Guangxi institute of oceanology Co., Ltd., Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Xiao Man
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi 535011, China
| | - Zenghou Xing
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi 535011, China
| | - Chongyang Wang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi 535011, China
| | - Congyan Yu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi 535011, China
| | - Jiamin Xing
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi 535011, China
| | - Xueyu Yan
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi 535011, China
| | - Hong Zhang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi 535011, China
| | - Mengqing Zeng
- Guangxi institute of oceanology Co., Ltd., Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Lei Bao
- Guangxi institute of oceanology Co., Ltd., Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Jie Zou
- Guangxi institute of oceanology Co., Ltd., Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Peng Zhu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi 535011, China.
| | - Youhou Xu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi 535011, China.
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Zhu Y, Hu S, Min J, Zhao Y, Yu H, Irfan M, Xu C. Transcriptomic analysis provides an insight into the function of CmGH9B3, a key gene of β-1, 4-glucanase, during the graft union healing of oriental melon scion grafted onto squash rootstock. Biotechnol J 2024; 19:e2400006. [PMID: 38581090 DOI: 10.1002/biot.202400006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 04/08/2024]
Abstract
The melon (Cucumis melo L.) is a globally cherished and economically significant crop. The grafting technique has been widely used in the vegetative propagation of melon to promote environmental tolerance and disease resistance. However, mechanisms governing graft healing and potential incompatibilities in melons following the grafting process remain unknown. To uncover the molecular mechanism of healing of grafted melon seedlings, melon wild type (Control) and TRV-CmGH9B3 lines were obtained and grafted onto the squash rootstocks (C. moschata). Anatomical differences indicated that the healing process of the TRV-CmGH9B3 plants was slower than that of the control. A total of 335 significantly differentially expressed genes (DEGs) were detected between two transcriptomes. Most of these DEGs were down-regulated in TRV-CmGH9B3 grafted seedlings. GO and KEGG analysis showed that many metabolic, physiological, and hormonal responses were involved in graft healing, including metabolic processes, plant hormone signaling, plant MAPK pathway, and sucrose starch pathway. During the healing process of TRV-CmGH9B3 grafted seedlings, gene synthesis related to hormone signal transduction (auxin, cytokinin, gibberellin, brassinolide) was delayed. At the same time, it was found that most of the DEGs related to the sucrose pathway were down-regulated in TRV-CmGH9B3 grafted seedlings. The results showed that sugar was also involved in the healing process of melon grafted onto squash. These results deepened our understanding of the molecular mechanism of GH9B3, a key gene of β-1, 4-glucanase. It also provided a reference for elucidating the gene mechanism and function analysis of CmGH9B3 in the process of graft union healing.
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Affiliation(s)
- Yulei Zhu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture (Ministry of Education), Shenyang, China
- Modern Protected Horticultural Engineering & Technology Center, Shenyang, China
| | - Shengwei Hu
- Hermiston Agricultural Research and Extension Station, Oregon State University, Hermiston, Oregon, USA
| | - Jiahuan Min
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture (Ministry of Education), Shenyang, China
- Modern Protected Horticultural Engineering & Technology Center, Shenyang, China
| | - Yingtong Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture (Ministry of Education), Shenyang, China
- Modern Protected Horticultural Engineering & Technology Center, Shenyang, China
| | - Hanqi Yu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture (Ministry of Education), Shenyang, China
- Modern Protected Horticultural Engineering & Technology Center, Shenyang, China
| | - Muhammad Irfan
- Department of Biotechnology, Faculty of science, University of Sargodha Pakistan, Sargodha, Pakistan
| | - Chuanqiang Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture (Ministry of Education), Shenyang, China
- Modern Protected Horticultural Engineering & Technology Center, Shenyang, China
- Key Laboratory of Horticultural Equipment (Ministry of Agriculture and Rural Affairs), Shenyang, China
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Zhang Y, He X, Mo X, Wu H, Zhao D. Similarities and differences: species and diet impact gut microbiota of captive pheasants. PeerJ 2024; 12:e16979. [PMID: 38560462 PMCID: PMC10979745 DOI: 10.7717/peerj.16979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 01/29/2024] [Indexed: 04/04/2024] Open
Abstract
The fecal microbiota plays an important role in maintaining animal health and is closely related to host life activities. In recent years, there have been an increasing number of studies on the fecal microbiota from birds. An exploration of the effects of species and living environments on the composition of gut microbiota will provide better protection for wildlife. In this study, non-injury sampling and 16S rDNA high-throughput sequencing were used to investigate the bacterial composition and diversity of the fecal microbiota in silver pheasants (Lophura nycthemera) and golden pheasants (Chrysolophus pictus) from Tianjin Zoo and Beijing Wildlife Park. The results showed that the abundance of Firmicutes was the highest in all fecal samples. At the genus level, Bacteroides was the common dominant bacteria, while there were some differences in other dominant bacteria genera. There were significant differences in fecal microbial composition between the golden pheasants from Tianjin Zoo and Beijing Wildlife Park. The metabolic analysis and functional prediction suggested that the gut microbiota composition and host metabolism were influenced by dietary interventions and living conditions. The results of this study provide the basis for further research of intestinal microbial of L. nycthemera and C. pictus, and valuable insights for conservation of related species.
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Affiliation(s)
- Yushuo Zhang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Xin He
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Xiuhong Mo
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Hong Wu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Dapeng Zhao
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
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Coleine C, Albanese D, Ray AE, Delgado-Baquerizo M, Stajich JE, Williams TJ, Larsen S, Tringe S, Pennacchio C, Ferrari BC, Donati C, Selbmann L. Metagenomics untangles potential adaptations of Antarctic endolithic bacteria at the fringe of habitability. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170290. [PMID: 38244622 DOI: 10.1016/j.scitotenv.2024.170290] [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: 11/21/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/22/2024]
Abstract
Survival and growth strategies of Antarctic endolithic microbes residing in Earth's driest and coldest desert remain virtually unknown. From 109 endolithic microbiomes, 4539 metagenome-assembled genomes were generated, 49.3 % of which were novel candidate bacterial species. We present evidence that trace gas oxidation and atmospheric chemosynthesis may be the prevalent strategies supporting metabolic activity and persistence of these ecosystems at the fringe of life and the limits of habitability.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy.
| | - Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Angelique E Ray
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Randwick, New South Wales 2052, Australia
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012 Sevilla, Spain; Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology and Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92507, USA; Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Randwick, New South Wales 2052, Australia
| | - Stefano Larsen
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Susannah Tringe
- Department of Energy Joint Genome Institute, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Christa Pennacchio
- Department of Energy Joint Genome Institute, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Randwick, New South Wales 2052, Australia
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy; Mycological Section, Italian Antarctic National Museum (MNA), Via al Porto Antico, 16128 Genoa, Italy
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Røken M, Iakhno S, Haaland AH, Bjelland AM, Wasteson Y. The Home Environment Is a Reservoir for Methicillin-Resistant Coagulase-Negative Staphylococci and Mammaliicocci. Antibiotics (Basel) 2024; 13:279. [PMID: 38534714 DOI: 10.3390/antibiotics13030279] [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: 02/13/2024] [Revised: 03/08/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
Coagulase-negative staphylococci (CoNS) and mammaliicocci are opportunistic human and animal pathogens, often resistant to multiple antimicrobials, including methicillin. Methicillin-resistant CoNS (MRCoNS) have traditionally been linked to hospitals and healthcare facilities, where they are significant contributors to nosocomial infections. However, screenings of non-hospital environments have linked MRCoNS and methicillin-resistant mammaliicocci (MRM) to other ecological niches. The aim of this study was to explore the home environment as a reservoir for MRCoNS and MRM. A total of 33 households, including households with a dog with a methicillin-resistant staphylococcal infection, households with healthy dogs or cats and households without pets, were screened for MRCoNS and MRM by sampling one human, one pet (if present) and the environment. Samples were analyzed by a selective culture-based method, and bacterial species were identified by MALDI-TOF MS and tested for antibiotic susceptibility by the agar disk diffusion method. Following whole-genome sequencing, a large diversity of SCCmec elements and sequence types was revealed, which did not indicate any clonal dissemination of specific strains. Virulome and mobilome analyses indicated a high degree of species specificity. Altogether, this study documents that the home environment is a reservoir for a variety of MRCoNS and MRM regardless of the type of household.
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Affiliation(s)
- Mari Røken
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
- Institute of Microbiology, Norwegian Armed Forces Joint Medical Services, 2027 Kjeller, Norway
| | | | - Anita Haug Haaland
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
- Regulations and Control Department, Animal Health, 0304 Oslo, Norway
| | - Ane Mohn Bjelland
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
- Department of Bacteriology, Norwegian Institute of Public Health, 0213 Oslo, Norway
| | - Yngvild Wasteson
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
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Wang Y, Xu Z, Zhang H, Zhou Y, Cao J, Zhang Y, Wang Z, Zhou J. Towards modelling tick-virus interactions using the weakly pathogenic Sindbis virus: Evidence that ticks are competent vectors. Front Cell Infect Microbiol 2024; 14:1334351. [PMID: 38567020 PMCID: PMC10985168 DOI: 10.3389/fcimb.2024.1334351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
Most tick-borne viruses (TBVs) are highly pathogenic and require high biosecurity, which severely limits their study. We found that Sindbis virus (SINV), predominantly transmitted by mosquitoes, can replicate in ticks and be subsequently transmitted, with the potential to serve as a model for studying tick-virus interactions. We found that both larval and nymphal stages of Rhipicephalus haemaphysaloides can be infected with SINV-wild-type (WT) when feeding on infected mice. SINV replicated in two species of ticks (R. haemaphysaloides and Hyalomma asiaticum) after infecting them by microinjection. Injection of ticks with SINV expressing enhanced Green Fluorescent Protein (eGFP) revealed that SINV-eGFP specifically aggregated in the tick midguts for replication. During blood-feeding, SINV-eGFP migrated from the midguts to the salivary glands and was transmitted to a new host. SINV infection caused changes in expression levels of tick genes related to immune responses, substance transport and metabolism, cell growth and death. SINV mainly induced autophagy during the early stage of infection; with increasing time of infection, the level of autophagy decreased, while the level of apoptosis increased. During the early stages of infection, the transcript levels of immune-related genes were significantly upregulated, and then decreased. In addition, SINV induced changes in the transcription levels of some functional genes that play important roles in the interactions between ticks and tick-borne pathogens. These results confirm that the SINV-based transmission model between ticks, viruses, and mammals can be widely used to unravel the interactions between ticks and viruses.
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Affiliation(s)
- Yanan Wang
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Zhengmao Xu
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Houshuang Zhang
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yongzhi Zhou
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Jie Cao
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yuqiang Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Zedong Wang
- Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Jilin, China
| | - Jinlin Zhou
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
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Dufault-Thompson K, Jiang X. Annotating microbial functions with ProkFunFind. mSystems 2024; 9:e0003624. [PMID: 38364094 PMCID: PMC10949468 DOI: 10.1128/msystems.00036-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/22/2024] [Indexed: 02/18/2024] Open
Abstract
Analyzing microbial genomes has become an essential part of microbiology research, giving valuable insights into the functions and evolution of microbial species. Identifying genes of interest and assigning putative annotations to those genes is a central task in genome analysis, and a plethora of tools and approaches have been developed for this task. The ProkFunFind tool was developed to bridge the gap between these various annotation approaches, providing a flexible and customizable search approach to annotate microbial functions. ProkFunFind is designed around hierarchical definitions of biological functions, where individual genes can be identified using heterogeneous search terms consisting of sequences, profile hidden Markov models, protein domains, and orthology groups. This flexible and customizable search approach allows for searches to be tailored to specific biological functions, and the search results are output in multiple formats to facilitate downstream analyses. The utility of the ProkFunFind search tool was demonstrated through its application in searching for bacterial flagella, which are complex organelles composed of multiple genes. Overall, ProkFunFind provides an accessible and flexible way to integrate multiple types of annotation and sequence data while annotating biological functions in microbial genomes.IMPORTANCEGenome sequencing and analysis are increasingly important parts of microbiology, providing a way to predict metabolic functions, identify virulence factors, and understand the evolution of microbes. The expanded use of genome sequencing has also brought an abundance of search and annotation methods, but integrating the information from these different methods can be challenging and is often done through ad hoc approaches. To bridge the gap between different types of annotations, we developed ProkFunFind, a flexible and customizable search tool incorporating multiple search approaches and annotation types to annotate microbial functions. We demonstrated the utility of ProkFunFind by searching for gene clusters encoding flagellar genes using a combination of different annotation types and searches. Overall, ProkFunFind provides a reproducible and flexible way to identify gene clusters of interest, facilitating the meaningful analysis of new and existing microbial genomes.
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Affiliation(s)
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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Purushothaman K, Crawford AD, Rocha SD, Göksu AB, Lange BM, Mydland LT, Vij S, Qingsong L, Øverland M, Press CM. Cyberlindnera jadinii yeast as a functional protein source: Modulation of immunoregulatory pathways in the intestinal proteome of zebrafish ( Danio rerio). Heliyon 2024; 10:e26547. [PMID: 38468924 PMCID: PMC10925985 DOI: 10.1016/j.heliyon.2024.e26547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 03/13/2024] Open
Abstract
Yeasts contain bioactive components that can enhance fish immune robustness and disease resistance. Our study focused on analyzing intestinal immunoregulatory pathways in zebrafish (Danio rerio) using iTRAQ and 2D LC-MS/MS to quantify intestinal proteins. Zebrafish were fed either control diet (C) or diet supplemented with autolyzed Cyberlindnera jadinii (ACJ). KEGG analysis revealed that ACJ yeast diet induced increased abundance of proteins related to arginine and proline metabolism, phagosome, C-lectin receptor signaling, ribosome and PPAR signaling pathways, which can modulate and enhance innate immune responses. ACJ yeast diet also showed decreased abundance of proteins associated with inflammatory pathways, including apoptosis, necroptosis and ferroptosis. These findings indicate boosted innate immune response and control of inflammation-related pathways in zebrafish intestine. Our findings in the well annotated proteome of zebrafish enabled a detailed investigation of intestinal responses and provide insight into health-beneficial effects of yeast species C. jadinii, which is relevant for aquaculture species.
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Affiliation(s)
- Kathiresan Purushothaman
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Alexander D. Crawford
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Sérgio D.C. Rocha
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway
| | - Aleksandar B. Göksu
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Byron Morales Lange
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway
| | - Liv Torunn Mydland
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway
| | - Shubha Vij
- School of Applied Science, Republic Polytechnic, 9 Woodlands Avenue 9, Singapore 738964, Singapore
- Tropical Futures Institute, James Cook University Singapore, 149 Sims Drive, 387380, Singapore
| | - Lin Qingsong
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Margareth Øverland
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway
| | - Charles McL. Press
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
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Meng C, Peng X, Zhang Y, Pedro GC, Li Y, Zhang Y, Duan Y, Sun X. Transcriptomic profiling of Poa pratensis L. under treatment of various phytohormones. Sci Data 2024; 11:297. [PMID: 38491031 PMCID: PMC10942976 DOI: 10.1038/s41597-024-03119-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
Poa pratensis L. (Poaceae) is a valuable grass across the north hemisphere, inhabiting diverse environments with wide altitudinal span, where ubiquitous various kinds of stresses. Phytohormones would be helpful to improve tolerance to abiotic and biotic stresses, but the responses of transcriptome regulation of P. pratensis to exogenous phytohormones application remain unclear. In this study, we explored the alteration of plant physiological responses by the application of phytohormones. Aiming to achieve this knowledge, we got full-length transcriptome data 42.76 Gb, of which 74.9% of transcripts were completed. Then used 27 samples representing four treatments conducted at two time points (1 h and 6 h after application) to generate RNA-seq data. 371 and 907 common DEGs were identified in response to four phytohormones application, respectively, these DEGs were involved in "plant hormone signal transduction", "carbon metabolism" and "plant-pathogen interaction". Finally, P. pratensis basic research can gain valuable information regarding the responses to exogenous application of phytohormones in physiological indicators and transcriptional regulations in order to facilitate the development of new cultivars.
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Affiliation(s)
- Chen Meng
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education and School of Life Sciences, Shaanxi Normal University, Xi'an, 710119, PR China
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomei Peng
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Zhang
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Yumeng Li
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanni Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education and School of Life Sciences, Shaanxi Normal University, Xi'an, 710119, PR China
| | - Yuanwen Duan
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Xudong Sun
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Sharma B, Sharma S, Medicherla KM, Reddy SM. Genome Sequence Analysis of Calcifying Bacteria Bacillus paranthracis CT5 and Its Biomineralization Efficacy to Improve the Strength and Durability Properties of Civil Structures. Curr Microbiol 2024; 81:109. [PMID: 38466427 DOI: 10.1007/s00284-024-03625-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 01/24/2024] [Indexed: 03/13/2024]
Abstract
Bacteria producing urea amidohydrolases (UA) and carbonic anhydrases (CA) are of great importance in civil engineering as these enzymes are responsible for microbially induced calcium carbonate precipitation (MICCP). In this investigation, genomic insights of Bacillus paranthracis CT5 and the expression of genes underlying in MICCP were studied. B. paranthracis produced a maximum level of UA (669.3 U/ml) and CA (125 U/ml) on 5th day of incubation and precipitated 197 mg/100 ml CaCO3 after 7 days of incubation. After 28 days of curing, compressive strength of bacterial admixed and bacterial cured (B-B) specimens was 13.7% higher compared to water-mixed and water-cured (W-W) specimens. A significant decrease in water absorption was observed in bacterial-cured specimens compared to water-cured specimens after 28 days of curing. For genome analysis, reads were assembled de novo producing 5,402,771 bp assembly with N50 of 273,050 bp. RAST annotation detected six amidohydrolase and three carbonic anhydrase genes. Among 5700 coding sequences found in genome, COG gene annotation grouped 4360 genes into COG categories with highest number of genes to transcription (435 genes), amino acid transport and metabolism (362 genes) along with cell wall/membrane/envelope biogenesis and ion transport and metabolism. KEGG functional classification predicted 223 pathways consisting of 1,960 genes and the highest number of genes belongs to two-component system (101 genes) and ABC transporter pathways (98 genes) enabling bacteria to sense and respond to environmental signals and actively transport various minerals and organic molecules, which facilitate the active transport of molecules required for MICCP.
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Affiliation(s)
- Bhavdeep Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, 147004, India
| | - Shruti Sharma
- Department of Civil Engineering, Thapar Institute of Engineering & Technology, Patiala, Punjab, 147004, India
| | | | - Sudhakara M Reddy
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, 147004, India.
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Stajich JE, Lovett B, Lee E, Macias AM, Hajek AE, de Bivort BL, Kasson MT, De Fine Licht HH, Elya C. Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.13.557621. [PMID: 37745330 PMCID: PMC10515909 DOI: 10.1101/2023.09.13.557621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. This is in part due to their large genome sizes and difficulty in obtaining sequenceable material. In this manuscript, we leveraged a recently-isolated, laboratory-tractable Entomophthora muscae isolate and improved long-read sequencing to obtain a largely-complete entomophthoralean genome. Our E. muscae assembly is 1.03 Gb, consists of 7,810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with other available (transcriptomic and genomic) datasets from entomophthoralean fungi, we provide new insight into the biology of these understudied pathogens. We offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex. Our findings suggest that substantial taxonomic revision is needed to define species within this group and we provide recommendations for differentiating strains and species in the context of the existing body of E. muscae scientific literature. We show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity, despite the presence of machinery to defend against transposable elements(RNAi). In addition, we find that E. muscae and its closest allies are enriched for M16A peptidases and possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We find that E. muscae has an expanded group of acid-trehalases, consistent with trehalose being the primary sugar component of fly (and insect) hemolymph. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae's species-specific, biotrophic lifestyle. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.
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Affiliation(s)
- Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA United States
| | - Brian Lovett
- Emerging Pests and Pathogens Research Unit, USDA-ARS, Ithaca, NY, United States
| | - Emily Lee
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Angie M. Macias
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Ann E. Hajek
- Department of Entomology, Cornell University, Ithaca, NY, United States
| | - Benjamin L. de Bivort
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Matt T. Kasson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Henrik H. De Fine Licht
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Carolyn Elya
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States
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Kirsch JM, Hryckowian AJ, Duerkop BA. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.06.561241. [PMID: 37873088 PMCID: PMC10592638 DOI: 10.1101/2023.10.06.561241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to insertion "hot spots" in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain level variation within the microbiota impacts human health.
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Affiliation(s)
- Joshua M. Kirsch
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, School of Medicine, Aurora, Colorado, 80045, USA
| | - Andrew J. Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53706, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53706, USA
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, School of Medicine, Aurora, Colorado, 80045, USA
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Wang Z, Zhou J, Zou J, Yang J, Chen W. Characterization of PYL gene family and identification of HaPYL genes response to drought and salt stress in sunflower. PeerJ 2024; 12:e16831. [PMID: 38464756 PMCID: PMC10924776 DOI: 10.7717/peerj.16831] [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: 07/03/2023] [Accepted: 01/04/2024] [Indexed: 03/12/2024] Open
Abstract
In the context of global climate change, drought and soil salinity are some of the most devastating abiotic stresses affecting agriculture today. PYL proteins are essential components of abscisic acid (ABA) signaling and play critical roles in responding to abiotic stressors, including drought and salt stress. Although PYL genes have been studied in many species, their roles in responding to abiotic stress are still unclear in the sunflower. In this study, 19 HaPYL genes, distributed on 15 of 17 chromosomes, were identified in the sunflower. Fragment duplication is the main cause of the expansion of PYL genes in the sunflower genome. Based on phylogenetic analysis, HaPYL genes were divided into three subfamilies. Members in the same subfamily share similar protein motifs and gene exon-intron structures, except for the second subfamily. Tissue expression patterns suggested that HaPYLs serve different functions when responding to developmental and environmental signals in the sunflower. Exogenous ABA treatment showed that most HaPYLs respond to an increase in the ABA level. Among these HaPYLs, HaPYL2a, HaPYL4d, HaPYL4g, HaPYL8a, HaPYL8b, HaPYL8c, HaPYL9b, and HaPYL9c were up-regulated with PEG6000 treatment and NaCl treatment. This indicates that they may play a role in resisting drought and salt stress in the sunflower by mediating ABA signaling. Our findings provide some clues to further explore the functions of PYL genes in the sunflower, especially with regards to drought and salt stress resistance.
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Affiliation(s)
- Zhaoping Wang
- China West Normal University, College of Life Sciences, Nanchong, Sichuan, China
| | - Jiayan Zhou
- China West Normal University, College of Life Sciences, Nanchong, Sichuan, China
| | - Jian Zou
- China West Normal University, College of Life Sciences, Nanchong, Sichuan, China
| | - Jun Yang
- China West Normal University, College of Life Sciences, Nanchong, Sichuan, China
| | - Weiying Chen
- China West Normal University, College of Life Sciences, Nanchong, Sichuan, China
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49
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Guerrero-Egido G, Pintado A, Bretscher KM, Arias-Giraldo LM, Paulson JN, Spaink HP, Claessen D, Ramos C, Cazorla FM, Medema MH, Raaijmakers JM, Carrión VJ. bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria. Nat Commun 2024; 15:2072. [PMID: 38453959 PMCID: PMC10920822 DOI: 10.1038/s41467-024-46302-y] [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: 07/13/2023] [Accepted: 02/21/2024] [Indexed: 03/09/2024] Open
Abstract
Bacteria have an extensive adaptive ability to live in close association with eukaryotic hosts, exhibiting detrimental, neutral or beneficial effects on host growth and health. However, the genes involved in niche adaptation are mostly unknown and their functions poorly characterized. Here, we present bacLIFE ( https://github.com/Carrion-lab/bacLIFE ) a streamlined computational workflow for genome annotation, large-scale comparative genomics, and prediction of lifestyle-associated genes (LAGs). As a proof of concept, we analyzed 16,846 genomes from the Burkholderia/Paraburkholderia and Pseudomonas genera, which led to the identification of hundreds of genes potentially associated with a plant pathogenic lifestyle. Site-directed mutagenesis of 14 of these predicted LAGs of unknown function, followed by plant bioassays, showed that 6 predicted LAGs are indeed involved in the phytopathogenic lifestyle of Burkholderia plantarii and Pseudomonas syringae pv. phaseolicola. These 6 LAGs encompassed a glycosyltransferase, extracellular binding proteins, homoserine dehydrogenases and hypothetical proteins. Collectively, our results highlight bacLIFE as an effective computational tool for prediction of LAGs and the generation of hypotheses for a better understanding of bacteria-host interactions.
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Affiliation(s)
- Guillermo Guerrero-Egido
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Adrian Pintado
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Kevin M Bretscher
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Luisa-Maria Arias-Giraldo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Joseph N Paulson
- Department of Data Sciences, N-Power Medicine, Redwood City, CA, 94063, USA
| | - Herman P Spaink
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Dennis Claessen
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Cayo Ramos
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
- Área de Genética, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
| | - Francisco M Cazorla
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Marnix H Medema
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Víctor J Carrión
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain.
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain.
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50
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Fabian B, Foster C, Asher A, Hassan K, Paulsen I, Tetu S. Identifying the suite of genes central to swimming in the biocontrol bacterium Pseudomonas protegens Pf-5. Microb Genom 2024; 10:001212. [PMID: 38546328 PMCID: PMC11004494 DOI: 10.1099/mgen.0.001212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/20/2024] [Indexed: 04/12/2024] Open
Abstract
Swimming motility is a key bacterial trait, important to success in many niches. Biocontrol bacteria, such as Pseudomonas protegens Pf-5, are increasingly used in agriculture to control crop diseases, where motility is important for colonization of the plant rhizosphere. Swimming motility typically involves a suite of flagella and chemotaxis genes, but the specific gene set employed for both regulation and biogenesis can differ substantially between organisms. Here we used transposon-directed insertion site sequencing (TraDIS), a genome-wide approach, to identify 249 genes involved in P. protegens Pf-5 swimming motility. In addition to the expected flagella and chemotaxis, we also identified a suite of additional genes important for swimming, including genes related to peptidoglycan turnover, O-antigen biosynthesis, cell division, signal transduction, c-di-GMP turnover and phosphate transport, and 27 conserved hypothetical proteins. Gene knockout mutants and TraDIS data suggest that defects in the Pst phosphate transport system lead to enhanced swimming motility. Overall, this study expands our knowledge of pseudomonad motility and highlights the utility of a TraDIS-based approach for analysing the functions of thousands of genes. This work sets a foundation for understanding how swimming motility may be related to the inconsistency in biocontrol bacteria performance in the field.
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Affiliation(s)
- B.K. Fabian
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - C. Foster
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - A. Asher
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - K.A. Hassan
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, Australia
| | - I.T. Paulsen
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - S.G. Tetu
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
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