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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; 55:1465-1476. [PMID: 38662153 PMCID: PMC11153388 DOI: 10.1007/s42770-024-01346-6] [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: 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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2
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Mastrantonio V, Libro P, Di Martino J, Matera M, Bellini R, Castrignanò T, Urbanelli S, Porretta D. Integrated de novo transcriptome of Culex pipiens mosquito larvae as a resource for genetic control strategies. Sci Data 2024; 11:471. [PMID: 38724521 PMCID: PMC11082219 DOI: 10.1038/s41597-024-03285-1] [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: 08/07/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
We present a de novo transcriptome of the mosquito vector Culex pipiens, assembled by sequences of susceptible and insecticide resistant larvae. The high quality of the assembly was confirmed by TransRate and BUSCO. A mapping percentage until 94.8% was obtained by aligning contigs to Nr, SwissProt, and TrEMBL, with 27,281 sequences that simultaneously mapped on the three databases. A total of 14,966 ORFs were also functionally annotated by using the eggNOG database. Among them, we identified ORF sequences of the main gene families involved in insecticide resistance. Therefore, this resource stands as a valuable reference for further studies of differential gene expression as well as to identify genes of interest for genetic-based control tools.
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Affiliation(s)
| | - Pietro Libro
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell'Università snc, 01100, Viterbo, Italy
| | - Jessica Di Martino
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell'Università snc, 01100, Viterbo, Italy
| | - Michele Matera
- Envu, 2022 ES Deutschland GmbH, Germany, Monheim, Germany
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Romeo Bellini
- Centro Agricoltura Ambiente "G. Nicoli", Via Sant'Agata 835, 40014, Crevalcore, Italy
| | - Tiziana Castrignanò
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell'Università snc, 01100, Viterbo, Italy.
| | - Sandra Urbanelli
- Department of Environmental Biology, Sapienza University of Rome, 00185, Rome, Italy
| | - Daniele Porretta
- Department of Environmental Biology, Sapienza University of Rome, 00185, Rome, Italy
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3
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Xu C, Xiang L, Huang W, Zhang X, Mao C, Wu S, Li T, Wang S, Wang S. Unraveling a Small Secreted Peptide SUBPEP3 That Positively Regulates Salt-Stress Tolerance in Pyrus betulifolia. Int J Mol Sci 2024; 25:4612. [PMID: 38731831 PMCID: PMC11083645 DOI: 10.3390/ijms25094612] [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: 03/14/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
Small secreted peptides (SSPs) play important roles in regulating plants' growth and development in response to external stimulus, but the genes and functions of SSPs in many species are still unknown. Therefore, it is particularly significant to characterize and annotate SSP genes in plant genomes. As a widely used stock of pears, Pyrus betulifolia has strong resistance to biotic and abiotic stresses. In this study, we analyzed the SSPs genes in the genome of P. betulifolia according to their characteristics and homology. A total of 1195 SSP genes were identified, and most of them are signaling molecules. Among these, we identified a new SSP, subtilase peptide 3 (SUBPEP3), which derived from the PA region of preSUBPEP3, increasing the expression level under salt stress. Both adding synthetic peptide SUBPEP3 to the culture medium of pears and the overexpression of SUBPEP3 in tobacco can improve the salt tolerance of plants. In summary, we annotated the SSP genes in the P. betulifolia genome and identified a small secreted peptide SUBPEP3 that regulates the salt tolerance of P. betulifolia, which provides an important theoretical basis for further revealing the function of SSPs.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Shengnan Wang
- College of Horticulture, China Agricultural University, Beijing 100080, China
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4
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Ma Y, Li J, Yu H, Teng L, Geng H, Li R, Xing R, Liu S, Li P. Comparative analysis of PacBio and ONT RNA sequencing methods for Nemopilema Nomurai venom identification. Genomics 2023; 115:110709. [PMID: 37739021 DOI: 10.1016/j.ygeno.2023.110709] [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: 05/26/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Recent studies on marine organisms have made use of third-generation sequencing technologies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). While these specialized bioinformatics tools have different algorithmic designs and performance capabilities, they offer scalability and can be applied to various datasets. We investigated the effectiveness of PacBio and ONT RNA sequencing methods in identifying the venom of the jellyfish species Nemopilema nomurai. We conducted a detailed analysis of the sequencing data from both methods, focusing on key characteristics such as CD, alternative splicing, long-chain noncoding RNA, simple sequence repeat, transcription factor, and functional transcript annotation. Our findings indicate that ONT generally produced higher raw data quality in the transcriptome analysis, while PacBio generated longer read lengths. PacBio was found to be superior in identifying CDs and long-chain noncoding RNA, whereas ONT was more cost-effective for predicting alternative splicing events, simple sequence repeats, and transcription factors. Based on these results, we conclude that PacBio is the most specific and sensitive method for identifying venom components, while ONT is the most cost-effective method for studying venogenesis, cnidocyst (venom gland) development, and transcription of virulence genes in jellyfish. Our study has implications for future sequencing technologies in marine jellyfish, and highlights the power of full-length transcriptome analysis in discovering potential therapeutic targets for jellyfish dermatitis.
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Affiliation(s)
- Yuzhen Ma
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Jie Li
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huahua Yu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China.
| | - Lichao Teng
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Geng
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongfeng Li
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Ronge Xing
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Song Liu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Pengcheng Li
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China.
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5
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Palomba M, Libro P, Di Martino J, Roca-Geronès X, Macali A, Castrignanò T, Canestrelli D, Mattiucci S. De novo transcriptome assembly of an Antarctic nematode for the study of thermal adaptation in marine parasites. Sci Data 2023; 10:720. [PMID: 37857654 PMCID: PMC10587230 DOI: 10.1038/s41597-023-02591-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Understanding the genomic underpinnings of thermal adaptation is a hot topic in eco-evolutionary studies of parasites. Marine heteroxenous parasites have complex life cycles encompassing a free-living larval stage, an ectothermic intermediate host and a homeothermic definitive host, thus representing compelling systems for the study of thermal adaptation. The Antarctic anisakid Contracaecum osculatum sp. D is a marine parasite able to survive and thrive both at very cold and warm temperatures within the environment and its hosts. Here, a de novo transcriptome of C. osculatum sp. D was generated for the first time, by performing RNA-Seq experiments on a set of individuals exposed to temperatures experienced by the nematode during its life cycle. The analysis generated 425,954,724 reads, which were assembled and then annotated. The high-quality assembly was validated, achieving over 88% mapping against the transcriptome. The transcriptome of this parasite will represent a valuable genomic resource for future studies aimed at disentangling the genomic architecture of thermal tolerance and metabolic pathways related to temperature stress.
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Affiliation(s)
- Marialetizia Palomba
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s/n, 01100, Viterbo, Italy
| | - Pietro Libro
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s/n, 01100, Viterbo, Italy
| | - Jessica Di Martino
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s/n, 01100, Viterbo, Italy
| | - Xavier Roca-Geronès
- Department of Biology, Health and Environment, Section of Parasitology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Joan XXIII Avenue, 27-31, 08028, Barcelona, Spain
| | - Armando Macali
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s/n, 01100, Viterbo, Italy
| | - Tiziana Castrignanò
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s/n, 01100, Viterbo, Italy.
| | - Daniele Canestrelli
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s/n, 01100, Viterbo, Italy
| | - Simonetta Mattiucci
- Department of Public Health and Infectious Diseases, Section of Parasitology, Sapienza University of Rome, P.le Aldo Moro, 5, 00185, Rome, Italy
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Fabbrini M, Scicchitano D, Candela M, Turroni S, Rampelli S. Connect the dots: sketching out microbiome interactions through networking approaches. MICROBIOME RESEARCH REPORTS 2023; 2:25. [PMID: 38058764 PMCID: PMC10696587 DOI: 10.20517/mrr.2023.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 12/08/2023]
Abstract
Microbiome networking analysis has emerged as a powerful tool for studying the complex interactions among microorganisms in various ecological niches, including the human body and several environments. This analysis has been used extensively in both human and environmental studies, revealing key taxa and functional units peculiar to the ecosystem considered. In particular, it has been mainly used to investigate the effects of environmental stressors, such as pollution, climate change or therapies, on host-associated microbial communities and ecosystem function. In this review, we discuss the latest advances in microbiome networking analysis, including methods for constructing and analyzing microbiome networks, and provide a case study on how to use these tools. These analyses typically involve constructing a network that represents interactions among microbial taxa or functional units, such as genes or metabolic pathways. Such networks can be based on a variety of data sources, including 16S rRNA sequencing, metagenomic sequencing, and metabolomics data. Once constructed, these networks can be analyzed to identify key nodes or modules important for the stability and function of the microbiome. By providing insights into essential ecological features of microbial communities, microbiome networking analysis has the potential to transform our understanding of the microbial world and its impact on human health and the environment.
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Affiliation(s)
- Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
- Authors contributed equally
| | - Daniel Scicchitano
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
- Authors contributed equally
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
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7
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Shams S, Ismaili A, Firouzabadi FN, Mumivand H, Sorkheh K. Comparative transcriptome analysis to identify putative genes involved in carvacrol biosynthesis pathway in two species of Satureja, endemic medicinal herbs of Iran. PLoS One 2023; 18:e0281351. [PMID: 37418504 PMCID: PMC10328369 DOI: 10.1371/journal.pone.0281351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 01/22/2023] [Indexed: 07/09/2023] Open
Abstract
Satureja is rich in phenolic monoterpenoids, mainly carvacrol, that is of interest due to diverse biological activities including antifungal and antibacterial. However, limited information is available regarding the molecular mechanisms underlying carvacrol biosynthesis and its regulation for this wonderful medicinal herb. To identify the putative genes involved in carvacrol and other monoterpene biosynthesis pathway, we generated a reference transcriptome in two endemic Satureja species of Iran, containing different yields (Satureja khuzistanica and Satureja rechingeri). Cross-species differential expression analysis was conducted between two species of Satureja. 210 and 186 transcripts related to terpenoid backbone biosynthesis were identified for S. khuzistanica and S. rechingeri, respectively. 29 differentially expressed genes (DEGs) involved in terpenoid biosynthesis were identified, and these DEGs were significantly enriched in monoterpenoid biosynthesis, diterpenoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, carotenoid biosynthesis and ubiquinone and other terpenoid-quinone biosynthesis pathways. Expression patterns of S. khuzistanica and S. rechingeri transcripts involved in the terpenoid biosynthetic pathway were evaluated. In addition, we identified 19 differentially expressed transcription factors (such as MYC4, bHLH, and ARF18) that may control terpenoid biosynthesis. We confirmed the altered expression levels of DEGs that encode carvacrol biosynthetic enzymes using quantitative real-time PCR (qRT-PCR). This study is the first report on de novo assembly and transcriptome data analysis in Satureja which could be useful for an understanding of the main constituents of Satureja essential oil and future research in this genus.
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Affiliation(s)
- Somayeh Shams
- Faculty of Agriculture, Department of Plant Production and Genetic Engineering, Lorestan University, Khorramabad, Iran
| | - Ahmad Ismaili
- Faculty of Agriculture, Department of Plant Production and Genetic Engineering, Lorestan University, Khorramabad, Iran
| | - Farhad Nazarian Firouzabadi
- Faculty of Agriculture, Department of Plant Production and Genetic Engineering, Lorestan University, Khorramabad, Iran
| | - Hasan Mumivand
- Faculty of Agriculture, Department of Horticultural Science, Lorestan University, Khorramabad, Iran
| | - Karim Sorkheh
- Faculty of Agriculture, Department of Plant Production and Genetic Engineering, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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Yang J, Wang S, Zhang Y, Chen Y, Zhou H, Zhang G. Identification, Culture Characteristics and Whole-Genome Analysis of Pestalotiopsis neglecta Causing Black Spot Blight of Pinus sylvestris var. mongolica. J Fungi (Basel) 2023; 9:jof9050564. [PMID: 37233276 DOI: 10.3390/jof9050564] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023] Open
Abstract
Black spot needle blight is a serious conifer disease of Pinus sylvestris var. mongolica occurring in Northeast China, which is usually caused by the plant pathogenic fungus Pestalotiopsis neglecta. From the diseased pine needles collected in Honghuaerji, the P. neglecta strain YJ-3 was isolated and identified as the phytopathogen, and its culture characteristics were studied. Then, we generated a highly contiguous 48.36-Mbp genome assembly (N50 = 6.62 Mbp) of the P. neglecta strain YJ-3 by combining the PacBio RS II Single Molecule Real Time (SMRT) and Illumina HiSeq X Ten sequencing platforms. The results showed that a total of 13,667 protein-coding genes were predicted and annotated using multiple bioinformatics databases. The genome assembly and annotation resource reported here will be useful for the study of fungal infection mechanisms and pathogen-host interaction.
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Affiliation(s)
- Jing Yang
- College of Forestry, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Shuren Wang
- Heilongjiang Province Key Laboratory of Forest Protection, School of Forest, Northeast Forestry University, Hexing Road 26, Xiangfang District, Harbin 150040, China
| | - Yundi Zhang
- Heilongjiang Province Key Laboratory of Forest Protection, School of Forest, Northeast Forestry University, Hexing Road 26, Xiangfang District, Harbin 150040, China
| | - Yunze Chen
- School of Biological Sciences, Guizhou Education University, Wudang District, Guiyang 550018, China
| | - Heying Zhou
- College of Forestry, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Guocai Zhang
- Heilongjiang Province Key Laboratory of Forest Protection, School of Forest, Northeast Forestry University, Hexing Road 26, Xiangfang District, Harbin 150040, China
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Photosynthetic and transcriptomic responses of Chlorella sp. to tigecycline. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
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10
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Das R, Tamang B, Najar IN, Thakur N, Mondal K. First report on metagenomics and their predictive functional analysis of fermented bamboo shoot food of Tripura, North East India. Front Microbiol 2023; 14:1158411. [PMID: 37125168 PMCID: PMC10130461 DOI: 10.3389/fmicb.2023.1158411] [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: 02/03/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Moiya pansung, mileye amileye, moiya koshak, and midukeye are naturally fermented bamboo shoot foods of Tripura. The present study aimed to reveal the whole microbial community structure of naturally fermented moiya pangsung, mileye amileye, moiya koshak, and midukeye along with the prediction of microbial functional profiles by shotgun metagenomic sequence analysis. The metataxonomic profile of moiya pangsung, mileye amileye, moiya koshak, and midukeye samples showed different domains, viz., bacteria (97.70%) followed by the virus (0.76%), unclassified (0.09%), eukaryotes (1.46%) and archaea (0.05%). Overall, 49 phyla, 409 families, 841 genera, and 1,799 species were found in all the fermented bamboo shoot samples collected from different places of Tripura. Firmicutes was the most abundant phylum (89.28%) followed by Proteobacteria (5.13%), Bacteroidetes (4.38%), Actinobacteria (1.02%), and Fusobacteria (0.17%). Lactiplantibacillus plantarum was the most abundant species in moiya pangsung, mileye amileye, moiya koshak, and midukeye followed by Lactococcus lactis, Levilactobacillus brevis, Leuconostoc mesenteroides, Weissella paramesenteroides, Leuconostoc kimchii, Pediococcus pentosaceus, Leuconostoc gasicomitatum, and Lacticaseibacillus casei. A few phyla of fungus were found, viz., Ascomycota, Basidiomycota, and Glomeromycota, where Ascomycota was present in high abundance. Functional analysis of moiya pangsung, mileye amileye, moiya koshak, and midukeye metagenome revealed the genes for the synthesis and metabolism of a wide range of bioactive compounds including, various essential amino acids, and conjugated amino acids. The abundance profile and predictive analysis of fermented bamboo shoots revealed a huge plethora of essential microorganisms and KEGG analysis revealed genes for amino acid metabolism, pectin degradation, lipid metabolism, and many other essential pathways that can be essential for the improvement of nutritional and sensory qualities of the fermented bamboo shoot products.
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Affiliation(s)
- Rohit Das
- Department of Microbiology, Sikkim University, Gangtok, India
| | - Buddhiman Tamang
- Department of Microbiology, Sikkim University, Gangtok, India
- *Correspondence: Buddhiman Tamang,
| | | | - Nagendra Thakur
- Department of Microbiology, Sikkim University, Gangtok, India
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11
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Zhang Z, Huang C, Du B, Xie C, Jiang L, Tang S, Xu X. Draft genome sequence of a new carotenoid-producing strain Brevibacterium sp. XU54, isolated from radioactive soil in Xinjiang, China. 3 Biotech 2022; 12:298. [PMID: 36276479 PMCID: PMC9522940 DOI: 10.1007/s13205-022-03366-1] [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: 03/13/2022] [Accepted: 09/17/2022] [Indexed: 11/01/2022] Open
Abstract
Some species of the genus Brevibacterium are orange bacteria involved in cheese ripening, synthesis of odoriferous compounds, and carotenoids with aromatic end groups. Here, we report the genome sequence of Brevibacterium sp. XU54, isolated from radioactive soil in Xinjiang, China. The genome of XU54 consists of 4,899,099 base pairs with a GC content of 62.2%. The genome sequence was annotated with 4453 genes, encoding 4260 proteins, 13 rRNAs, and 49 tRNAs. 16S rRNA BLAST and comparative genomic analysis both indicated that XU54 may be a new species of Brevibacterium. In addition, compared to the type strains, some enzymes related to sulfur metabolism showed a low similarity of 66.85, 79.53 and 14.61%, respectively. The carotenoids biosynthesis gene cluster was identified and analyzed according to the genomic data, which revealed relatively low identity (5-85%) with existing strains. The optimum conditions for its growth and carotenoid production were then discussed. The whole-genome sequence of Brevibacterium sp. XU54 will be beneficial for utilizing these newly identified genes in carotenoid biosynthesis and regulation of sulfur metabolism pathway to promote the production of novel carotenoids and other structurally diverse compounds through combinatorial biosynthesis, which facilitates cheese ripening and coloration. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03366-1.
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Affiliation(s)
- Zhidong Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | - Chunyan Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046 Jiangsu China
| | - Bangmian Du
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046 Jiangsu China
| | - Chengjia Xie
- School of Chemical Engineering, Yangzhou Polytechnic Institute, Yangzhou, 225127 Jiangsu China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | - Susu Tang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | - Xian Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046 Jiangsu China
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Tong J, Ji X, Zhang H, Xiong B, Cui D, Jiang L. The Analysis of the Ubiquitylomic Responses to Streptococcus agalactiae Infection in Bovine Mammary Gland Epithelial Cells. J Inflamm Res 2022; 15:4331-4343. [PMID: 35923910 PMCID: PMC9342659 DOI: 10.2147/jir.s368779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/19/2022] [Indexed: 01/21/2023] Open
Abstract
Purpose Streptococcus agalactiae is one of the primary pathogens responsible for subclinical mastitis, a significant economic burden for dairy farms. An essential component of the immune response to infection is ubiquitination, which plays important roles in the complex interactions between the pathogen and host. Materials and Methods In the present study, quantitative ubiquitylomics was performed to profile changes in the global ubiquitinome of bovine mammary gland epithelial cells (BMECs) infected with S. agalactiae. Results The most notable changes in the BMEC ubiquitinome were related to the adherens junction, ribosome, and tight junction pathways. Ubiquitination of CTNNB1, EGFR, ITGB1, CTNNA1, CTNNA2, CDH1, YES1, and SLC9A3R1 appears to be fundamental for regulating multiple cellular processes in BMECs in response to S. agalactiae infection. In addition, broad ubiquitination of various effectors and outer membrane proteins was observed. Ubiquitinated proteins in S. agalactiae-infected BMECs were associated with regulating cell junctions in the host, with potential implications for susceptibility to infection. Conclusion The preliminary findings suggest that extensive ubiquitination of CTNNB1, CDH1 and SLC9A3R1 and proteins closely related to cell junctions might play an important role in mastitis progression in dairy cows. The results provide evidence that ubiquitin modification of certain proteins in S. agalactiae-infected BMECs could be a promising therapeutic strategy for reducing mammary gland injury and mastitis.
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Affiliation(s)
- Jinjin Tong
- Beijing Key Laboratory for Dairy Cow Nutrition, Beijing University of Agriculture, Beijing, People’s Republic of China
| | - Xintong Ji
- Beijing Key Laboratory for Dairy Cow Nutrition, Beijing University of Agriculture, Beijing, People’s Republic of China
| | - Hua Zhang
- Beijing Key Laboratory for Dairy Cow Nutrition, Beijing University of Agriculture, Beijing, People’s Republic of China
| | - Benhai Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Defeng Cui
- Beijing Key Laboratory of TCVM, Beijing University of Agriculture, Beijing, People’s Republic of China
- Correspondence: Defeng Cui, Beijing Key Laboratory of TCVM, Beijing University of Agriculture, Beijing, People’s Republic of China, Tel +86 (10)-81798091, Email
| | - Linshu Jiang
- Beijing Key Laboratory for Dairy Cow Nutrition, Beijing University of Agriculture, Beijing, People’s Republic of China
- Linshu Jiang, Beijing Key Laboratory for Dairy Cow Nutrition, Beijing University of Agriculture, Beijing, People’s Republic of China, Tel +86 (10)-81798091, Email
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13
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Bogaert KA, Blomme J, Beeckman T, De Clerck O. Auxin's origin: do PILS hold the key? TRENDS IN PLANT SCIENCE 2022; 27:227-236. [PMID: 34716098 DOI: 10.1016/j.tplants.2021.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 08/23/2021] [Accepted: 09/28/2021] [Indexed: 05/12/2023]
Abstract
Auxin is a key regulator of many developmental processes in land plants and plays a strikingly similar role in the phylogenetically distant brown seaweeds. Emerging evidence shows that the PIN and PIN-like (PILS) auxin transporter families have preceded the evolution of the canonical auxin response pathway. A wide conservation of PILS-mediated auxin transport, together with reports of auxin function in unicellular algae, would suggest that auxin function preceded the advent of multicellularity. We find that PIN and PILS transporters form two eukaryotic subfamilies within a larger bacterial family. We argue that future functional characterisation of algal PIN and PILS transporters can shed light on a common origin of an auxin function followed by independent co-option in a multicellular context.
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Affiliation(s)
- Kenny Arthur Bogaert
- Department of Biology, Ghent University, Krijgslaan 281 S8, B-9000 Ghent, Belgium.
| | - Jonas Blomme
- Department of Biology, Ghent University, Krijgslaan 281 S8, B-9000 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB-UGent, Technologiepark 72, B-9052 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB-UGent, Technologiepark 72, B-9052 Ghent, Belgium
| | - Olivier De Clerck
- Department of Biology, Ghent University, Krijgslaan 281 S8, B-9000 Ghent, Belgium
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14
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Saheb Kashaf S, Proctor DM, Deming C, Saary P, Hölzer M, Taylor ME, Kong HH, Segre JA, Almeida A, Finn RD. Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions. Nat Microbiol 2022; 7:169-179. [PMID: 34952941 PMCID: PMC8732310 DOI: 10.1038/s41564-021-01011-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 10/28/2021] [Indexed: 12/23/2022]
Abstract
Human skin functions as a physical barrier to foreign pathogen invasion and houses numerous commensals. Shifts in the human skin microbiome have been associated with conditions ranging from acne to atopic dermatitis. Previous metagenomic investigations into the role of the skin microbiome in health or disease have found that much of the sequenced data do not match reference genomes, making it difficult to interpret metagenomic datasets. We combined bacterial cultivation and metagenomic sequencing to assemble the Skin Microbial Genome Collection (SMGC), which comprises 622 prokaryotic species derived from 7,535 metagenome-assembled genomes and 251 isolate genomes. The metagenomic datasets that we generated were combined with publicly available skin metagenomic datasets to identify members and functions of the human skin microbiome. The SMGC collection includes 174 newly identified bacterial species and 12 newly identified bacterial genera, including the abundant genus 'Candidatus Pellibacterium', which has been newly associated with the skin. The SMGC increases the characterized set of known skin bacteria by 26%. We validated the SMGC metagenome-assembled genomes by comparing them with sequenced isolates obtained from the same samples. We also recovered 12 eukaryotic species and assembled thousands of viral sequences, including newly identified clades of jumbo phages. The SMGC enables classification of a median of 85% of skin metagenomic sequences and provides a comprehensive view of skin microbiome diversity, derived primarily from samples obtained in North America.
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Affiliation(s)
- Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Diana M Proctor
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clay Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul Saary
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Martin Hölzer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Monica E Taylor
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Heidi H Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Alexandre Almeida
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
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15
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Zhong S, Sang L, Zhao Z, Deng Y, Liu H, Yu Y, Liu J. Phosphoproteome analysis reveals the involvement of protein dephosphorylation in ethylene-induced corolla senescence in petunia. BMC PLANT BIOLOGY 2021; 21:512. [PMID: 34732145 PMCID: PMC8565076 DOI: 10.1186/s12870-021-03286-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Senescence represents the last stage of flower development. Phosphorylation is the key posttranslational modification that regulates protein functions, and kinases may be more required than phosphatases during plant growth and development. However, little is known about global phosphorylation changes during flower senescence. RESULTS In this work, we quantitatively investigated the petunia phosphoproteome following ethylene or air treatment. In total, 2170 phosphosites in 1184 protein groups were identified, among which 2059 sites in 1124 proteins were quantified. To our surprise, treatment with ethylene resulted in 697 downregulated and only 117 upregulated phosphosites using a 1.5-fold threshold (FDR < 0.05), which showed that ethylene negatively regulates global phosphorylation levels and that phosphorylation of many proteins was not necessary during flower senescence. Phosphoproteome analysis showed that ethylene regulates ethylene and ABA signalling transduction pathways via phosphorylation levels. One of the major targets of ethylene-induced dephosphorylation is the plant mRNA splicing machinery, and ethylene treatment increases the number of alternative splicing events of precursor RNAs in petunia corollas. CONCLUSIONS Protein dephosphorylation could play an important role in ethylene-induced senescence, and ethylene treatment increased the number of AS precursor RNAs in petunia corollas.
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Affiliation(s)
- Shiwei Zhong
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
- School of Landscape Architecture School of Tourism and Health, Zhejiang A & F University, Zhejiang, 311300 Hangzhou China
| | - Lina Sang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Zhixia Zhao
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Ying Deng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Haitao Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Yixun Yu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642 China
| | - Juanxu Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
- School of Landscape Architecture School of Tourism and Health, Zhejiang A & F University, Zhejiang, 311300 Hangzhou China
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16
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Yu C, Lian B, Fang W, Guo A, Ke Y, Jiang Y, Chen Y, Liu G, Zhong F, Zhang J. Transcriptome-based analysis reveals that the biosynthesis of anthocyanins is more active than that of flavonols and proanthocyanins in the colorful flowers of Lagerstroemia indica. Biol Futur 2021; 72:473-488. [PMID: 34554492 DOI: 10.1007/s42977-021-00094-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 07/16/2021] [Indexed: 11/30/2022]
Abstract
Mechanisms associated with the control of flower color in crape myrtle varieties have yet to be sufficiently elucidated, which has tended to hamper the use of modern molecular and genetic strategies in the breeding programs for this plant. The whole transcriptome of four L. indica varieties characterized by different flower colors (white, light purple, deep purplish pink, and strong red) was sequenced, and we performed bioinformatic, quantitative PCR, and co-expression analyses of R2R3 MYB transcription factor and anthocyanin/flavonol pathway genes. We obtained a total of 49,980 transcripts with full-length coding sequences. Both transcriptome and qPCR analyses revealed that anthocyanin/flavonol pathway genes were differentially expressed among the four different flowers types, with the expression of LiPAL, LiCHS, LiCHI, LiDFR, LiANS/LDOX, and LiUFGT being induced in colorful flowers, whereas that of LiF3´5´H, LiFLS, and LiLAR was found to be inhibited. Base on phylogenetic analysis, seven R2R3 MYB transcriptional factors were identified as putative regulators of flower color. The molecular characteristics and co-expression patterns indicated that these MYBs differentially modulate their target genes, with two probably acting as activators, three as repressors, and one contributing to the regulation of vacuolar pH. The findings of this study indicate that the anthocyanin biosynthesis is more active than the flavonol and proanthocyanin in the colorful flowers. These observations provide new genomic information on L. indica and contribute gene resources for the flower color-targeted breeding of crape myrtle.
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Affiliation(s)
- Chunmei Yu
- Key Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, 226019, Jiangsu Province, China
| | - Bolin Lian
- Key Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, 226019, Jiangsu Province, China
| | - Wei Fang
- Key Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, 226019, Jiangsu Province, China
| | - Anfang Guo
- Key Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, 226019, Jiangsu Province, China
| | - Yongchao Ke
- Key Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, 226019, Jiangsu Province, China
| | - Yuna Jiang
- Key Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, 226019, Jiangsu Province, China
| | - Yanhong Chen
- Key Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, 226019, Jiangsu Province, China
| | - Guoyuan Liu
- Key Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, 226019, Jiangsu Province, China
| | - Fei Zhong
- Key Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, 226019, Jiangsu Province, China
| | - Jian Zhang
- Key Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, 226019, Jiangsu Province, China.
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Cho SH, Jeong Y, Lee E, Ko SR, Ahn CY, Oh HM, Cho BK, Cho S. Assessment of Erythrobacter Species Diversity through Pan-Genome Analysis with Newly Isolated Erythrobacter sp. 3-20A1M. J Microbiol Biotechnol 2021; 31:601-609. [PMID: 33526758 PMCID: PMC9723273 DOI: 10.4014/jmb.2012.12054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/15/2022]
Abstract
Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pangenome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species. The presence of virulence genes, especially the plant-algae cell wall degrading genes, revealed that Erythrobacter sp. 3-20A1M is a potential marine plant-algae scavenger.
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Affiliation(s)
- Sang-Hyeok Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yujin Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Eunju Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - So-Ra Ko
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Chi-Yong Ahn
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Hee-Mock Oh
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea,KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea,
B.-K. Cho E-mail:
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea,KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea,Corresponding authors S. Cho Phone: +82-42-350-2660 Fax: +82-42-350-5620 E-mail:
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18
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Chen C, Fu R, Wang J, Li X, Chen X, Li Q, Lu D. Genome sequence and transcriptome profiles of pathogenic fungus Paecilomyces penicillatus reveal its interactions with edible fungus Morchella importuna. Comput Struct Biotechnol J 2021; 19:2607-2617. [PMID: 34025947 PMCID: PMC8120865 DOI: 10.1016/j.csbj.2021.04.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 12/15/2022] Open
Abstract
Paecilomyces penicillatus is one of the pathogens of morels, which greatly affects the yield and quality of Morchella spp.. In the present study, we de novo assembled the genome sequence of the fungus P. penicillatus SAAS_ppe1. We analyzed the transcriptional profile of P. penicillatus SAAS_ppe1 infection of Morchella importuna at different stages (3 days and 6 days after infection) and the response of M. importuna using the transcriptome. The assembled genome sequence of P. penicillatus SAAS_ppe1 was 39.78 Mb in length (11 scaffolds; scaffold N50, 6.50 Mb), in which 99.7% of the expected genes were detected. A total of 7.48% and 19.83% clean transcriptional reads from the infected sites were mapped to the P. penicillatus genome at the early and late stages of infection, respectively. There were 3,943 genes differently expressed in P. penicillatus at different stages of infection, of which 24 genes had increased expression with the infection and infection stage, including diphthamide biosynthesis, aldehyde reductase, and NAD (P)H-hydrate epimerase (P < 0.05). Several genes had variable expression trends at different stages of infection, indicating P. penicillatus had diverse regulation patterns to infect M. importuna. GO function, involving cellular components, and KEGG pathways, involving glycerolipid metabolism, and plant-pathogen interaction were significantly enriched during infection by P. penicillatus. The expression of ten genes in M. importuna increased during the infection and infection stage, and these may regulate the response of M. importuna to P. penicillatus infection. This is the first comprehensive study on P. penicillatus infection mechanism and M. importuna response mechanism, which will lay a foundation for understanding the fungus-fungus interactions, gene functions, and variety breeding of pathogenic and edible fungi.
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Affiliation(s)
- Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, PR China
| | - Rongtao Fu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, PR China
| | - Jian Wang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, PR China
| | - Xingyue Li
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, PR China
| | - Xiaojuan Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, PR China
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, PR China
| | - Daihua Lu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, PR China
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He H, Miao R, Huang L, Jiang H, Cheng Y. Vegetative cells may perform nitrogen fixation function under nitrogen deprivation in Anabaena sp. strain PCC 7120 based on genome-wide differential expression analysis. PLoS One 2021; 16:e0248155. [PMID: 33662009 PMCID: PMC7932525 DOI: 10.1371/journal.pone.0248155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/20/2021] [Indexed: 11/25/2022] Open
Abstract
Nitrogen assimilation is strictly regulated in cyanobacteria. In an inorganic nitrogen-deficient environment, some vegetative cells of the cyanobacterium Anabaena differentiate into heterocysts. We assessed the photosynthesis and nitrogen-fixing capacities of heterocysts and vegetative cells, respectively, at the transcriptome level. RNA extracted from nitrogen-replete vegetative cells (NVs), nitrogen-deprived vegetative cells (NDVs), and nitrogen-deprived heterocysts (NDHs) in Anabaena sp. strain PCC 7120 was evaluated by transcriptome sequencing. Paired comparisons of NVs vs. NDHs, NVs vs. NDVs, and NDVs vs. NDHs revealed 2,044 differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes enrichment analysis of the DEGs showed that carbon fixation in photosynthetic organisms and several nitrogen metabolism-related pathways were significantly enriched. Synthesis of Gvp (Gas vesicle synthesis protein gene) in NVs was blocked by nitrogen deprivation, which may cause Anabaena cells to sink and promote nitrogen fixation under anaerobic conditions; in contrast, heterocysts may perform photosynthesis under nitrogen deprivation conditions, whereas the nitrogen fixation capability of vegetative cells was promoted by nitrogen deprivation. Immunofluorescence analysis of nitrogenase iron protein suggested that the nitrogen fixation capability of vegetative cells was promoted by nitrogen deprivation. Our findings provide insight into the molecular mechanisms underlying nitrogen fixation and photosynthesis in vegetative cells and heterocysts at the transcriptome level. This study provides a foundation for further functional verification of heterocyst growth, differentiation, and water bloom control.
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Affiliation(s)
- Hongli He
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin Province, China
| | - Runyu Miao
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin Province, China
| | - Lilong Huang
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin Province, China
| | - Hongshan Jiang
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin Province, China
| | - Yunqing Cheng
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin Province, China
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Muturi SM, Muthui LW, Njogu PM, Onguso JM, Wachira FN, Opiyo SO, Pelle R. Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya. PLoS One 2021; 16:e0244755. [PMID: 33395690 PMCID: PMC7781671 DOI: 10.1371/journal.pone.0244755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/16/2020] [Indexed: 12/27/2022] Open
Abstract
The obstacle to optimal utilization of biogas technology is poor understanding of biogas microbiomes diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. Randomized complete block design was utilized to assign the twelve treatments to four blocks, within eastern and central regions of Kenya. We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversity studies. We identified 37 phyla, 65 classes and 132 orders. Bacteria dominated and comprised 28 phyla, 42 classes and 92 orders, conveying substrate's versatility in the treatments. Though, Fungi and Archaea comprised 5 phyla, the Fungi were richer; suggesting the importance of hydrolysis and fermentation in biogas production. High β-diversity within the taxa was largely linked to communities' metabolic capabilities. Clostridiales and Bacteroidales, the most prevalent guilds, metabolize organic macromolecules. The identified Cytophagales, Alteromonadales, Flavobacteriales, Fusobacteriales, Deferribacterales, Elusimicrobiales, Chlamydiales, Synergistales to mention but few, also catabolize macromolecules into smaller substrates to conserve energy. Furthermore, δ-Proteobacteria, Gloeobacteria and Clostridia affiliates syntrophically regulate PH2 and reduce metal to provide reducing equivalents. Methanomicrobiales and other Methanomicrobia species were the most prevalence Archaea, converting formate, CO2(g), acetate and methylated substrates into CH4(g). Thermococci, Thermoplasmata and Thermoprotei were among the sulfur and other metal reducing Archaea that contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, comprising largely Ascomycota and Basidiomycota species. Chytridiomycetes, Blastocladiomycetes and Mortierellomycetes were among the rare species, suggesting their metabolic and substrates limitations. Generally, we observed that environmental and treatment perturbations influenced communities' abundance, β-diversity and reactor performance largely through stochastic effect. Understanding diversity of biogas microbiomes over wide environmental variables and its' productivity provided insights into better management strategies that ameliorate biochemical limitations to effective biogas production.
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Affiliation(s)
- Samuel Mwangangi Muturi
- Department of Biological Sciences, University of Eldoret, Eldoret, Kenya
- Institute for Bioteschnology Research, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Lucy Wangui Muthui
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Paul Mwangi Njogu
- Institute for Energy and Environmental Technology, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Justus Mong’are Onguso
- Institute for Bioteschnology Research, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | | | - Stephen Obol Opiyo
- OARDC, Molecular and Cellular Imaging Center-Columbus, Ohio State University, Columbus, Ohio, United States of America
- The University of Sacread Heart, Gulu, Uganda
| | - Roger Pelle
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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Shi K, Li J, Lv J, Liu P, Li J, Li S. Full-length transcriptome sequences of ridgetail white prawn Exopalaemon carinicauda provide insight into gene expression dynamics during thermal stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 747:141238. [PMID: 32799022 DOI: 10.1016/j.scitotenv.2020.141238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/10/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Marine heat waves and extreme high temperature become more frequent and intense in these years, which affected the survival of aquaculture animals. The ridgetail white prawn Exopalaemon carinicauda is an important economic species in eastern China, which has remarkable thermal tolerance. However, there has been little study of its thermal-adaptation mechanisms due to the complex genetic structure and unknown genome. To better understand the molecular mechanisms of E. carinicauda to adapt to the changing temperature, a combination of Illumina-based short reads RNA-seq and single molecule real-time-based full-length transcriptome sequencing was used in this study. In total, 17,212 unigenes from high-quality transcripts of E. carinicauda were generated and 14,663 complete ORFs were detected with an average length of 1980 bp. In addition, the transcriptome profiles of E. carinicauda treated with 34 °C heat stress for 6 and 24 h were analyzed. These differentially expressed genes were primarily enriched in oxidation-reduction process (Gene Ontology enrichment, GO) and the pathways of starch and sucrose metabolism (Kyoto Encyclopedia of Genes and Genomes enrichment, KEGG) after 6 h thermal stress, which indicated that E. carinicauda was suffering the attack by reactive oxygen species. After 24 h thermal stress, these differentially expressed genes were enriched in the pathway of lysosome, glycine, serine and threonine metabolism, fatty acid metabolism (KEGG), which indicated the oxidative stress was decreased. Interestingly, 40 genes for hemocyanin were found to be downregulated after 6 h heat stress, which indicated that the immunocompetence of E. carinicauda decreased after short term thermal stress (6 h). After 24 h thermal stress, E. carinicauda showed transcriptional adaptation to high temperature by upregulating of 11 genes encoding molecular chaperones, including HSP40 and HSP90 which were firstly reported to be related to thermal stress in E. carinicauda. These results promote a better understanding of the thermal-adaptation mechanism of E. carinicauda.
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Affiliation(s)
- Kunpeng Shi
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Jitao Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Jianjian Lv
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Ping Liu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Jian Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China.
| | - Sedong Li
- Guangdong Evergreen Ltd. Corporation, Zhanjiang, PR China
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Yang X, Zhu ZH, Ji X, Liu ZM, Zhang H, Wei B. Complete genome sequence of Micromonospora craniellae LHW63014 T, a potential metal ion-chelating agent producer. Mar Genomics 2020; 57:100830. [PMID: 33160875 DOI: 10.1016/j.margen.2020.100830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 10/23/2022]
Abstract
Micromonospora craniellae LHW63014T is a novel marine Micromonospora, isolated from a Craniella species sponge collected in the South China Sea. In this study, we report the complete genome sequence of M. craniellae LHW63014T, which is comprised of a circular chromosome of 6,839,926 bp with the G + C content of 70.9 mol%. The complete genome contained 6572 protein-coding genes, 48 tRNA genes, and 9 rRNA genes. Genomic annotations revealed that 79.09% of the protein-coding genes were assigned to the COG database, among which, the abundant genes were predicted to be involved in transcription, replication, recombination and repair, and amino acid transport and metabolism. Secondary metabolites prediction using antiSMASH revealed that 22 biosynthetic gene clusters (BGC) of secondary metabolites were located in the genome of M. craniellae LHW63014T, 19 of which showed low similarity (<50%) to known BGCs and 5 of which showed the closest homology with BGCs encoding metal ion-chelating agents, indicating the immense potential of M. craniellae LHW63014T to produce a wide variety of novel antibiotics, especially for metal ion-chelating agents.
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Affiliation(s)
- Xue Yang
- School of Pharmacy, Qilu Medical University, Zibo 255300, PR China
| | - Zhong-Hui Zhu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xia Ji
- School of Pharmacy, Qilu Medical University, Zibo 255300, PR China
| | - Zhao-Ming Liu
- School of Pharmacy, Qilu Medical University, Zibo 255300, PR China
| | - Hua Zhang
- School of Pharmacy, Qilu Medical University, Zibo 255300, PR China
| | - Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, PR China.
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23
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Yin SS, Gao FH. Molecular Mechanism of Tumor Cell Immune Escape Mediated by CD24/Siglec-10. Front Immunol 2020; 11:1324. [PMID: 32765491 PMCID: PMC7379889 DOI: 10.3389/fimmu.2020.01324] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022] Open
Abstract
Tumor immune escape is an important part of tumorigenesis and development. Tumor cells can develop a variety of immunosuppressive mechanisms to combat tumor immunity. Exploring tumor cells that escape immune surveillance through the molecular mechanism of related immunosuppression in-depth is helpful to develop the treatment strategies of targeted tumor immune escape. The latest studies show that CD24 on the surface of tumor cells interacts with Siglec-10 on the surface of immune cells to promote the immune escape of tumor cells. It is necessary to comment on the molecular mechanism of inhibiting the activation of immune cells through the interaction between CD24 on tumor cells and Siglec-10 on immune cells, and a treatment strategy of tumors through targeting CD24 on the surface of tumor cells or Siglec-10 on immune cells.
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Affiliation(s)
- Shan-Shan Yin
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feng-Hou Gao
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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24
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Fu FF, Hao Z, Wang P, Lu Y, Xue LJ, Wei G, Tian Y, Hu B, Xu H, Shi J, Cheng T, Wang G, Yi Y, Chen J. Genome Sequence and Comparative Analysis of Colletotrichum gloeosporioides Isolated from Liriodendron Leaves. PHYTOPATHOLOGY 2020; 110:1260-1269. [PMID: 32202483 DOI: 10.1094/phyto-12-19-0452-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Colletotrichum gloeosporioides is a hemibiotrophic pathogen causing significant losses to economically important crops and forest trees, including Liriodendron. To explore the interaction between C. gloeosporioides and Liriodendron and to identify the candidate genes determining the pathogenesis, we sequenced and assembled the whole genome of C. gloeosporioides Lc1 (CgLc1) using PacBio and Illumina next generation sequencing and performed a comparative genomic analysis between CgLc1 and Cg01, the latter being a described endophytic species of the C. gloeosporioides complex. Gene structure prediction identified 15,744 protein-coding genes and 837 noncoding RNAs. Species-specific genes were characterized using an ortholog analysis followed by a pathway enrichment analysis, which showed that genes specific to CgLc1 were enriched for the arginine biosynthetic process. Furthermore, genome synteny analysis revealed that most of the protein-coding genes fell into collinear blocks. However, two clusters of polyketide synthase genes were identified to be specific for CgLc1, suggesting that they might have an important role in virulence control. Transcriptional regulators coexpressed with polyketide synthase genes were detected through a Weighted Correlation Network Analysis. Taken together, this work provides new insight into the virulence- and pathogenesis-associated genes present in C. gloeosporioides and its possible lifestyle.
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Affiliation(s)
- Fang-Fang Fu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Pengkai Wang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Ye Lu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Liang-Jiao Xue
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Guoyu Wei
- Shanghai Municipal Agricultural and Rural Affairs Commission, Shanghai, China
| | - Yanli Tian
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Baishi Hu
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Haibin Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Tielong Cheng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Guibin Wang
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yin Yi
- State Forestry Administration Key Laboratory of Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, China
- Guizhou Provincial Key Laboratory of Plant Physiology and Developmental Regulation, Guizhou Normal University, Guiyang, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
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Vascon S, Frasca M, Tripodi R, Valentini G, Pelillo M. Protein function prediction as a graph-transduction game. Pattern Recognit Lett 2020. [DOI: 10.1016/j.patrec.2018.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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26
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Gu Z, Men S, Zhu J, Hao Q, Tong N, Liu ZA, Zhang H, Shu Q, Wang L. Chalcone synthase is ubiquitinated and degraded via interactions with a RING-H2 protein in petals of Paeonia 'He Xie'. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4749-4762. [PMID: 31106836 PMCID: PMC6760318 DOI: 10.1093/jxb/erz245] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/12/2019] [Indexed: 05/07/2023]
Abstract
Flavonoids are secondary metabolites widely distributed among angiosperms, where they play diverse roles in plant growth, development, and evolution. The regulation of flavonoid biosynthesis in plants has been extensively studied at the transcriptional level, but post-transcriptional, translational, and post-translational control of flavonoid biosynthesis remain poorly understood. In this study, we analysed post-translational regulation of flavonoid biosynthesis in the ornamental plant Paeonia, using proteome and ubiquitylome profiling, in conjunction with transcriptome data. Three enzymes involved in flavonoid biosynthesis were identified as being putative targets of ubiquitin-mediated degradation. Among these, chalcone synthase (PhCHS) was shown to have the greatest number of ubiquitination sites. We examined PhCHS abundance in petals using PhCHS-specific antibody and found that its accumulation decreased at later developmental stages, resulting from 26S proteasome-mediated degradation. We further identified a ring domain-containing protein (PhRING-H2) that physically interacts with PhCHS and demonstrated that PhRING-H2 is required for PhCHS ubiquitination. Taken together, our results suggest that PhRING-H2-mediates PhCHS ubiquitination and degradation is an important mechanism of post-translational regulation of flavonoid biosynthesis in Paeonia, providing a theoretical basis for the manipulation of flavonoid biosynthesis in plants.
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Affiliation(s)
- Zhaoyu Gu
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Siqi Men
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Jin Zhu
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Qing Hao
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ningning Tong
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Zheng-An Liu
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hechen Zhang
- Horticulture Institute of He’nan Academy of Agricultural Sciences, Zhengzhou, China
| | - Qingyan Shu
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Correspondence: or
| | - Liangsheng Wang
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
- Correspondence: or
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27
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Bewick S, Gurarie E, Weissman JL, Beattie J, Davati C, Flint R, Thielen P, Breitwieser F, Karig D, Fagan WF. Trait-based analysis of the human skin microbiome. MICROBIOME 2019; 7:101. [PMID: 31277701 PMCID: PMC6612184 DOI: 10.1186/s40168-019-0698-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 05/19/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND The past decade of microbiome research has concentrated on cataloging the diversity of taxa in different environments. The next decade is poised to focus on microbial traits and function. Most existing methods for doing this perform pathway analysis using reference databases. This has both benefits and drawbacks. Function can go undetected if reference databases are coarse-grained or incomplete. Likewise, detection of a pathway does not guarantee expression of the associated function. Finally, function cannot be connected to specific microbial constituents, making it difficult to ascertain the types of organisms exhibiting particular traits-something that is important for understanding microbial success in specific environments. A complementary approach to pathway analysis is to use the wealth of microbial trait information collected over years of lab-based, culture experiments. METHODS Here, we use journal articles and Bergey's Manual of Systematic Bacteriology to develop a trait-based database for 971 human skin bacterial taxa. We then use this database to examine functional traits that are over/underrepresented among skin taxa. Specifically, we focus on three trait classes-binary, categorical, and quantitative-and compare trait values among skin taxa and microbial taxa more broadly. We compare binary traits using a Chi-square test, categorical traits using randomization trials, and quantitative traits using a nonparametric relative effects test based on global rankings using Tukey contrasts. RESULTS We find a number of traits that are over/underrepresented within the human skin microbiome. For example, spore formation, acid phosphatase, alkaline phosphatase, pigment production, catalase, and oxidase are all less common among skin taxa. As well, skin bacteria are less likely to be aerobic, favoring, instead, a facultative strategy. They are also less likely to exhibit gliding motility, less likely to be spirillum or rod-shaped, and less likely to grow in chains. Finally, skin bacteria have more difficulty at high pH, prefer warmer temperatures, and are much less resilient to hypotonic conditions. CONCLUSIONS Our analysis shows how an approach that relies on information from culture experiments can both support findings from pathway analysis, and also generate new insights into the structuring principles of microbial communities.
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Affiliation(s)
- Sharon Bewick
- Department of Biological Sciences, Clemson University, Clemson, SC 29631 USA
| | - Eliezer Gurarie
- Department of Biology, University of Maryland, College Park, MD 20742 USA
| | - JL Weissman
- Department of Biology, University of Maryland, College Park, MD 20742 USA
| | - Jess Beattie
- Department of Biology, University of Maryland, College Park, MD 20742 USA
| | - Cyrus Davati
- Department of Biology, University of Maryland, College Park, MD 20742 USA
| | - Rachel Flint
- Department of Biology, University of Maryland, College Park, MD 20742 USA
| | - Peter Thielen
- Research and Exploratory Development Department, Johns Hopkins Applied Physics Laboratory, Laurel, MD 20723 USA
| | - Florian Breitwieser
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205 USA
| | - David Karig
- Research and Exploratory Development Department, Johns Hopkins Applied Physics Laboratory, Laurel, MD 20723 USA
- Department of Bioengineering, Clemson University, Clemson, SC 29631 USA
| | - William F. Fagan
- Department of Biology, University of Maryland, College Park, MD 20742 USA
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Parey E, Crombach A. Evolution of the Drosophila melanogaster Chromatin Landscape and Its Associated Proteins. Genome Biol Evol 2019; 11:660-677. [PMID: 30689829 PMCID: PMC6411481 DOI: 10.1093/gbe/evz019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2019] [Indexed: 12/30/2022] Open
Abstract
In the nucleus of eukaryotic cells, genomic DNA associates with numerous protein complexes and RNAs, forming the chromatin landscape. Through a genome-wide study of chromatin-associated proteins in Drosophila cells, five major chromatin types were identified as a refinement of the traditional binary division into hetero- and euchromatin. These five types were given color names in reference to the Greek word chroma. They are defined by distinct but overlapping combinations of proteins and differ in biological and biochemical properties, including transcriptional activity, replication timing, and histone modifications. In this work, we assess the evolutionary relationships of chromatin-associated proteins and present an integrated view of the evolution and conservation of the fruit fly Drosophila melanogaster chromatin landscape. We combine homology prediction across a wide range of species with gene age inference methods to determine the origin of each chromatin-associated protein. This provides insight into the evolution of the different chromatin types. Our results indicate that for the euchromatic types, YELLOW and RED, young associated proteins are more specialized than old ones; and for genes found in either chromatin type, intron/exon structure is lineage-specific. Next, we provide evidence that a subset of GREEN-associated proteins is involved in a centromere drive in D. melanogaster. Our results on BLUE chromatin support the hypothesis that the emergence of Polycomb Group proteins is linked to eukaryotic multicellularity. In light of these results, we discuss how the regulatory complexification of chromatin links to the origins of eukaryotic multicellularity.
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Affiliation(s)
- Elise Parey
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Université Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Anton Crombach
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Université Paris, France.,Inria, Antenne Lyon La Doua, Villeurbanne, France.,Université de Lyon, INSA-Lyon, LIRIS, UMR 5205, Villeurbanne, France
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29
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Couto-Rodríguez RL, Montalvo-Rodríguez R. Temporal Analysis of the Microbial Community from the Crystallizer Ponds in Cabo Rojo, Puerto Rico, Using Metagenomics. Genes (Basel) 2019; 10:E422. [PMID: 31159288 PMCID: PMC6627146 DOI: 10.3390/genes10060422] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 01/21/2023] Open
Abstract
The Cabo Rojo solar salterns are a hypersaline environment located in a tropical climate, where conditions remain stable throughout the year. These conditions can favor the establishment of steady microbial communities. Little is known about the microbial composition that thrives in hypersaline environments in the tropics. The main goal of this study was to assess the microbial diversity present in the crystallizer ponds of Cabo Rojo, in terms of structure and metabolic processes across time using metagenomic techniques. Three samplings (December 2014, March and July 2016) were carried out, where water samples (50 L each) were filtered through a Millipore pressurized filtering system. DNA was subsequently extracted using physical-chemical methods and sequenced using paired end Illumina technologies. The sequencing effort produced three paired end libraries with a total of 111,816,040 reads, that were subsequently assembled into three metagenomes. Out of the phyla detected, the microbial diversity was dominated in all three samples by Euryarchaeota, followed by Bacteroidetes and Proteobacteria. However, sample MFF1 (for Muestreo Final Fraternidad) exhibited a higher diversity, with 12 prokaryotic phyla detected at 34% NaCl (w/v), when compared to samples MFF2 and MFF3, which only exhibited three phyla. Precipitation events might be one of the contributing factors to the change in the microbial community composition through time. Diversity at genus level revealed a more stable community structure, with an overwhelming dominance of the square archaeon Haloquadratum in the three metagenomes. Furthermore, functional annotation was carried out in order to detect genes related to metabolic processes, such as carbon, nitrogen, and sulfur cycles. The presence of gene sequences related to nitrogen fixation, ammonia oxidation, sulfate reduction, sulfur oxidation, and phosphate solubilization were detected. Through binning methods, four putative novel genomes were obtained, including a possible novel genus belonging to the Bacteroidetes and possible new species for the genera Natronomonas, Halomicrobium, and Haloquadratum. Using a metagenomic approach, a 3-year study has been performed in a Caribbean hypersaline environment. When compared to other salterns around the world, the Cabo Rojo salterns harbor a similar community composition, which is stable through time. Moreover, an analysis of gene composition highlights the importance of the microbial community in the biogeochemical cycles at hypersaline environments.
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Affiliation(s)
- Ricardo L Couto-Rodríguez
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603, USA.
- Biology Department, Box 9000, University of Puerto Rico, Mayagüez, PR 00681, USA.
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Abstract
The distinction between orthologs and paralogs, genes that started diverging by speciation versus duplication, is relevant in a wide range of contexts, most notably phylogenetic tree inference and protein function annotation. In this chapter, we provide an overview of the methods used to infer orthology and paralogy. We survey both graph-based approaches (and their various grouping strategies) and tree-based approaches, which solve the more general problem of gene/species tree reconciliation. We discuss conceptual differences among the various orthology inference methods and databases and examine the difficult issue of verifying and benchmarking orthology predictions. Finally, we review typical applications of orthologous genes, groups, and reconciled trees and conclude with thoughts on future methodological developments.
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31
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Revealing the influence of microbiota on the quality of Pu-erh tea during fermentation process by shotgun metagenomic and metabolomic analysis. Food Microbiol 2018; 76:405-415. [DOI: 10.1016/j.fm.2018.07.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 06/27/2018] [Accepted: 07/01/2018] [Indexed: 11/17/2022]
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32
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Sheikhizadeh Anari S, de Ridder D, Schranz ME, Smit S. Efficient inference of homologs in large eukaryotic pan-proteomes. BMC Bioinformatics 2018; 19:340. [PMID: 30257640 PMCID: PMC6158922 DOI: 10.1186/s12859-018-2362-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 09/09/2018] [Indexed: 12/31/2022] Open
Abstract
Background Identification of homologous genes is fundamental to comparative genomics, functional genomics and phylogenomics. Extensive public homology databases are of great value for investigating homology but need to be continually updated to incorporate new sequences. As new sequences are rapidly being generated, there is a need for efficient standalone tools to detect homologs in novel data. Results To address this, we present a fast method for detecting homology groups across a large number of individuals and/or species. We adopted a k-mer based approach which considerably reduces the number of pairwise protein alignments without sacrificing sensitivity. We demonstrate accuracy, scalability, efficiency and applicability of the presented method for detecting homology in large proteomes of bacteria, fungi, plants and Metazoa. Conclusions We clearly observed the trade-off between recall and precision in our homology inference. Favoring recall or precision strongly depends on the application. The clustering behavior of our program can be optimized for particular applications by altering a few key parameters. The program is available for public use at https://github.com/sheikhizadeh/pantools as an extension to our pan-genomic analysis tool, PanTools. Electronic supplementary material The online version of this article (10.1186/s12859-018-2362-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
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33
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Ma R, Liu F, Yap SF, Lee H, Leong RW, Riordan SM, Grimm MC, Zhang L. The Growth and Protein Expression of Inflammatory Bowel Disease-Associated Campylobacter concisus Is Affected by the Derivatives of the Food Additive Fumaric Acid. Front Microbiol 2018; 9:896. [PMID: 29867807 PMCID: PMC5966568 DOI: 10.3389/fmicb.2018.00896] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/18/2018] [Indexed: 12/22/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic inflammatory conditions of the gastrointestinal tract with multifactorial etiology. Both dietary factors and the microbe Campylobacter concisus have been found to be associated with the condition. The current study examined the effects of sodium fumarate, a neutralized product of the food additives fumaric acid and monosodium fumarate when in the intestinal environment, on the growth of C. concisus to determine the effects of these food additives on IBD-associated bacterial species. Through culture methods and quantification, it was found that neutralized fumaric acid, neutralized monosodium fumarate, and sodium fumarate increased the growth of C. concisus, with the greatest increase in growth at a concentration of 0.4%. Further examination of 50 C. concisus strains on media with added sodium fumarate showed that greatest growth was also achieved at a concentration of 0.4%. At a concentration of 2% sodium fumarate, all strains examined displayed less growth in comparison with those cultured on media without sodium fumarate. Using mass spectrometry, multiple C. concisus proteins showed significant differential expression when cultured on media with and without 0.4% sodium fumarate. The findings presented suggest that patients with IBD should consider avoiding excessive consumption of foods with fumaric acid or its sodium salts, and that the addition of 0.4% sodium fumarate alone to media may assist in the isolation of C. concisus from clinical samples.
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Affiliation(s)
- Rena Ma
- The School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Fang Liu
- The School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Soe F Yap
- The School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Hoyul Lee
- The School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Rupert W Leong
- Concord Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Stephen M Riordan
- Gastrointestinal and Liver Unit, The Prince of Wales Hospital, Sydney, NSW, Australia
| | - Michael C Grimm
- St George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Li Zhang
- The School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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Galpert D, Fernández A, Herrera F, Antunes A, Molina-Ruiz R, Agüero-Chapin G. Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers. BMC Bioinformatics 2018; 19:166. [PMID: 29724166 PMCID: PMC5934817 DOI: 10.1186/s12859-018-2148-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/04/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog classification approach implemented in a big data platform that considered several pairwise protein features and the low ortholog pair ratios found between two annotated proteomes (Galpert, D et al., BioMed Research International, 2015). The supervised models were built and tested using a Saccharomycete yeast benchmark dataset proposed by Salichos and Rokas (2011). Despite several pairwise protein features being combined in a supervised big data approach; they all, to some extent were alignment-based features and the proposed algorithms were evaluated on a unique test set. Here, we aim to evaluate the impact of alignment-free features on the performance of supervised models implemented in the Spark big data platform for pairwise ortholog detection in several related yeast proteomes. RESULTS The Spark Random Forest and Decision Trees with oversampling and undersampling techniques, and built with only alignment-based similarity measures or combined with several alignment-free pairwise protein features showed the highest classification performance for ortholog detection in three yeast proteome pairs. Although such supervised approaches outperformed traditional methods, there were no significant differences between the exclusive use of alignment-based similarity measures and their combination with alignment-free features, even within the twilight zone of the studied proteomes. Just when alignment-based and alignment-free features were combined in Spark Decision Trees with imbalance management, a higher success rate (98.71%) within the twilight zone could be achieved for a yeast proteome pair that underwent a whole genome duplication. The feature selection study showed that alignment-based features were top-ranked for the best classifiers while the runners-up were alignment-free features related to amino acid composition. CONCLUSIONS The incorporation of alignment-free features in supervised big data models did not significantly improve ortholog detection in yeast proteomes regarding the classification qualities achieved with just alignment-based similarity measures. However, the similarity of their classification performance to that of traditional ortholog detection methods encourages the evaluation of other alignment-free protein pair descriptors in future research.
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Affiliation(s)
- Deborah Galpert
- Departamento de Ciencia de la Computación, Universidad Central ¨Marta Abreu¨ de Las Villas (UCLV), 54830, Santa Clara, Cuba
| | - Alberto Fernández
- Department of Computer Science and Artificial Intelligence, Research Center on Information and Communications Technology (CITIC-UGR), University of Granada, 18071, Granada, Spain
| | - Francisco Herrera
- Department of Computer Science and Artificial Intelligence, Research Center on Information and Communications Technology (CITIC-UGR), University of Granada, 18071, Granada, Spain
| | - Agostinho Antunes
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n 4450-208 Matosinhos, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Reinaldo Molina-Ruiz
- Centro de Bioactivos Químicos (CBQ), Universidad Central ¨Marta Abreu¨ de Las Villas (UCLV), 54830, Santa Clara, Cuba
| | - Guillermin Agüero-Chapin
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n 4450-208 Matosinhos, Porto, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal. .,Centro de Bioactivos Químicos (CBQ), Universidad Central ¨Marta Abreu¨ de Las Villas (UCLV), 54830, Santa Clara, Cuba.
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Gao L, Wu K, Liu Z, Yao X, Yuan S, Tao W, Yi L, Yu G, Hou Z, Fan D, Tian Y, Liu J, Chen ZJ, Liu J. Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution. Cell 2018. [PMID: 29526463 DOI: 10.1016/j.cell.2018.02.028] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The dynamics of the chromatin regulatory landscape during human early embryogenesis remains unknown. Using DNase I hypersensitive site (DHS) sequencing, we report that the chromatin accessibility landscape is gradually established during human early embryogenesis. Interestingly, the DHSs with OCT4 binding motifs are enriched at the timing of zygotic genome activation (ZGA) in humans, but not in mice. Consistently, OCT4 contributes to ZGA in humans, but not in mice. We further find that lower CpG promoters usually establish DHSs at later stages. Similarly, younger genes tend to establish promoter DHSs and are expressed at later embryonic stages, while older genes exhibit these features at earlier stages. Moreover, our data show that human active transposons SVA and HERV-K harbor DHSs and are highly expressed in early embryos, but not in differentiated tissues. In summary, our data provide an evolutionary developmental view for understanding the regulation of gene and transposon expression.
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Affiliation(s)
- Lei Gao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Keliang Wu
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Zhenbo Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Xuelong Yao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Shenli Yuan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Wenrong Tao
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Lizhi Yi
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Guanling Yu
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Zhenzhen Hou
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Dongdong Fan
- Key Laboratory of RNA Biology of CAS, University of Chinese Academy of Sciences, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yong Tian
- Key Laboratory of RNA Biology of CAS, University of Chinese Academy of Sciences, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jianqiao Liu
- Center for Reproductive Medicine, Third Affiliated Hospital, Guangzhou Medical University, 510150 Guangzhou, China.
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China.
| | - Jiang Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, 100049 Beijing, China.
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36
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Imchen M, Kumavath R, Barh D, Azevedo V, Ghosh P, Viana M, Wattam AR. Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems. Sci Rep 2017; 7:8859. [PMID: 28821820 PMCID: PMC5562921 DOI: 10.1038/s41598-017-09254-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 07/26/2017] [Indexed: 02/06/2023] Open
Abstract
In this study, we categorize the microbial community in mangrove sediment samples from four different locations within a vast mangrove system in Kerala, India. We compared this data to other samples taken from the other known mangrove data, a tropical rainforest, and ocean sediment. An examination of the microbial communities from a large mangrove forest that stretches across southwestern India showed strong similarities across the higher taxonomic levels. When ocean sediment and a single isolate from a tropical rain forest were included in the analysis, a strong pattern emerged with Bacteria from the phylum Proteobacteria being the prominent taxon among the forest samples. The ocean samples were predominantly Archaea, with Euryarchaeota as the dominant phylum. Principal component and functional analyses grouped the samples isolated from forests, including those from disparate mangrove forests and the tropical rain forest, from the ocean. Our findings show similar patterns in samples were isolated from forests, and these were distinct from the ocean sediment isolates. The taxonomic structure was maintained to the level of class, and functional analysis of the genes present also displayed these similarities. Our report for the first time shows the richness of microbial diversity in the Kerala coast and its differences with tropical rain forest and ocean microbiome.
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Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Periye, Padanakkad P.O, Kasaragod, Kerala, 671314, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Periye, Padanakkad P.O, Kasaragod, Kerala, 671314, India.
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, 721172, India.,Xcode Life Sciences, 3D Eldorado, 112 Nungambakkam High Road, Nungambakkam, Chennai, Tamil Nadu, 600034, India.,Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, Virginia, 23284, USA
| | - Marcus Viana
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Alice R Wattam
- Biocomplexity Institute, Virginia Tech University, Blacksburg, Virginia, 24061, USA.
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Vera Alvarez R, Medeiros Vidal N, Garzón-Martínez GA, Barrero LS, Landsman D, Mariño-Ramírez L. Workflow and web application for annotating NCBI BioProject transcriptome data. Database (Oxford) 2017; 2017:3737827. [PMID: 28605765 PMCID: PMC5467576 DOI: 10.1093/database/bax008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/21/2016] [Accepted: 01/24/2017] [Indexed: 01/08/2023]
Abstract
Abstract The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. Database URL: http://www.ncbi.nlm.nih.gov/projects/physalis/.
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Affiliation(s)
- Roberto Vera Alvarez
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike. Bethesda, MD 20894, USA
| | - Newton Medeiros Vidal
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike. Bethesda, MD 20894, USA
| | - Gina A. Garzón-Martínez
- Colombian Corporation for Agricultural Research (CORPOICA), Km 14 vía Mosquera, Bogota, Colombia
| | - Luz S. Barrero
- Colombian Corporation for Agricultural Research (CORPOICA), Km 14 vía Mosquera, Bogota, Colombia
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike. Bethesda, MD 20894, USA
| | - Leonardo Mariño-Ramírez
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike. Bethesda, MD 20894, USA
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Guo J, Liu J, Wei Q, Wang R, Yang W, Ma Y, Chen G, Yu Y. Proteomes and Ubiquitylomes Analysis Reveals the Involvement of Ubiquitination in Protein Degradation in Petunias. PLANT PHYSIOLOGY 2017; 173:668-687. [PMID: 27810942 PMCID: PMC5210702 DOI: 10.1104/pp.16.00795] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 11/02/2016] [Indexed: 05/04/2023]
Abstract
Petal senescence is a complex programmed process. It has been demonstrated previously that treatment with ethylene, a plant hormone involved in senescence, can extensively alter transcriptome and proteome profiles in plants. However, little is known regarding the impact of ethylene on posttranslational modification (PTM) or the association between PTM and the proteome. Protein degradation is one of the hallmarks of senescence, and ubiquitination, a major PTM in eukaryotes, plays important roles in protein degradation. In this study, we first obtained reference petunia (Petunia hybrida) transcriptome data via RNA sequencing. Next, we quantitatively investigated the petunia proteome and ubiquitylome and the association between them in petunia corollas following ethylene treatment. In total, 51,799 unigenes, 3,606 proteins, and 2,270 ubiquitination sites were quantified 16 h after ethylene treatment. Treatment with ethylene resulted in 14,448 down-regulated and 6,303 up-regulated unigenes (absolute log2 fold change > 1 and false discovery rate < 0.001), 284 down-regulated and 233 up-regulated proteins, and 320 up-regulated and 127 down-regulated ubiquitination sites using a 1.5-fold threshold (P < 0.05), indicating that global ubiquitination levels increase during ethylene-mediated corolla senescence in petunia. Several putative ubiquitin ligases were up-regulated at the protein and transcription levels. Our results showed that the global proteome and ubiquitylome were negatively correlated and that ubiquitination could be involved in the degradation of proteins during ethylene-mediated corolla senescence in petunia. Ethylene regulates hormone signaling transduction pathways at both the protein and ubiquitination levels in petunia corollas. In addition, our results revealed that ethylene increases the ubiquitination levels of proteins involved in endoplasmic reticulum-associated degradation.
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Affiliation(s)
- Jianhang Guo
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
| | - Juanxu Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
| | - Qian Wei
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
| | - Rongmin Wang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
| | - Weiyuan Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
| | - Yueyue Ma
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
| | - Guoju Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
| | - Yixun Yu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China
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Transcriptome Sequencing of Gynostemma pentaphyllum to Identify Genes and Enzymes Involved in Triterpenoid Biosynthesis. Int J Genomics 2016; 2016:7840914. [PMID: 28097124 PMCID: PMC5206855 DOI: 10.1155/2016/7840914] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/29/2016] [Accepted: 11/07/2016] [Indexed: 01/13/2023] Open
Abstract
G. pentaphyllum (Gynostemma pentaphyllum), a creeping herbaceous perennial with many important medicinal properties, is widely distributed in Asia. Gypenosides (triterpenoid saponins), the main effective components of G. pentaphyllum, are well studied. FPS (farnesyl pyrophosphate synthase), SS (squalene synthase), and SE (squalene epoxidase) are the main enzymes involved in the synthesis of triterpenoid saponins. Considering the important medicinal functions of G. pentaphyllum, it is necessary to investigate the transcriptomic information of G. pentaphyllum to facilitate future studies of transcriptional regulation. After sequencing G. pentaphyllum, we obtained 50,654,708 unigenes. Next, we used RPKM (reads per kilobases per million reads) to calculate expression of the unigenes and we performed comparison of our data to that contained in five common databases to annotate different aspects of the unigenes. Finally, we noticed that FPS, SS, and SE showed differential expression of enzymes in DESeq. Leaves showed the highest expression of FPS, SS, and SE relative to the other two tissues. Our research provides transcriptomic information of G. pentaphyllum in its natural environment and we found consistency in unigene expression, enzymes expression (FPS, SS, and SE), and the distribution of gypenosides content in G. pentaphyllum. Our results will enable future related studies of G. pentaphyllum.
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Warden JG, Casaburi G, Omelon CR, Bennett PC, Breecker DO, Foster JS. Characterization of Microbial Mat Microbiomes in the Modern Thrombolite Ecosystem of Lake Clifton, Western Australia Using Shotgun Metagenomics. Front Microbiol 2016; 7:1064. [PMID: 27458453 PMCID: PMC4933708 DOI: 10.3389/fmicb.2016.01064] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/24/2016] [Indexed: 12/02/2022] Open
Abstract
Microbialite-forming communities interact with the environment and influence the precipitation of calcium carbonate through their metabolic activity. The functional genes associated with these metabolic processes and their environmental interactions are therefore critical to microbialite formation. The microbiomes associated with microbialite-forming ecosystems are just now being elucidated and the extent of shared pathways and taxa across different environments is not fully known. In this study, we profiled the microbiome of microbial communities associated with lacustrine thrombolites located in Lake Clifton, Western Australia using metagenomic sequencing and compared it to the non-lithifying mats associated with surrounding sediments to determine whether differences in the mat microbiomes, particularly with respect to metabolic pathways and environmental interactions, may potentially contribute to thrombolite formation. Additionally, we used stable isotope biosignatures to delineate the dominant metabolism associated with calcium carbonate precipitation in the thrombolite build-ups. Results indicated that the microbial community associated with the Lake Clifton thrombolites was predominantly bacterial (98.4%) with Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria comprising the majority of annotated reads. Thrombolite-associated mats were enriched in photoautotrophic taxa and functional genes associated with photosynthesis. Observed δ13C values of thrombolite CaCO3 were enriched by at least 3.5‰ compared to theoretical values in equilibrium with lake water DIC, which is consistent with the occurrence of photoautotrophic activity in thrombolite-associated microbial mats. In contrast, the microbiomes of microbial communities found on the sandy non-lithifying sediments of Lake Clifton represented distinct microbial communities that varied in taxa and functional capability and were enriched in heterotrophic taxa compared to the thrombolite-associated mats. This study provides new insight into the taxa and functional capabilities that differentiate potentially lithifying mats from other non-lithifying types and suggests that thrombolites are actively accreting and growing in limited areas of Lake Clifton.
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Affiliation(s)
- John G Warden
- Department of Geological Sciences, University of Texas at Austin, AustinTX, USA; Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Merritt IslandFL, USA
| | - Giorgio Casaburi
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Merritt Island FL, USA
| | - Christopher R Omelon
- Department of Geological Sciences, University of Texas at Austin, Austin TX, USA
| | - Philip C Bennett
- Department of Geological Sciences, University of Texas at Austin, Austin TX, USA
| | - Daniel O Breecker
- Department of Geological Sciences, University of Texas at Austin, Austin TX, USA
| | - Jamie S Foster
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Merritt Island FL, USA
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41
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Ren Y, Palusiak A, Wang W, Wang Y, Li X, Wei H, Kong Q, Rozalski A, Yao Z, Wang Q. A High-resolution Typing Assay for Uropathogenic Escherichia coli Based on Fimbrial Diversity. Front Microbiol 2016; 7:623. [PMID: 27199951 PMCID: PMC4850163 DOI: 10.3389/fmicb.2016.00623] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/15/2016] [Indexed: 02/02/2023] Open
Abstract
Urinary tract infections (UTIs) are one of the most common bacterial infections in humans, causing cystitis, pyelonephritis, and renal failure. Uropathogenic Escherichia coli (UPEC) is the leading cause of UTIs. Accurate and rapid discrimination of UPEC lineages is useful for epidemiological surveillance. Fimbriae are necessary for the adherence of UPEC strains to host uroepithelia, and seem to be abundant and diverse in UPEC strains. By analyzing all the possible fimbrial operons in UPEC strains, we found that closely related strains had similar types of chaperone-usher fimbriae, and the diversity of fimbrial genes was higher than that of multilocus sequence typing (MLST) genes. A typing assay based on the polymorphism of four gene sequences (three fimbrial genes and one housekeeping gene) and the diversity of fimbriae present was developed. By comparison with the MLST, whole-genome sequence (WGS) and fumC/fimH typing methods, this was shown to be accurate and have high resolution, and it was also relatively inexpensive and easy to perform. The assay can supply more discriminatory information for UPEC lineages, and have the potential to be applied in epidemiological surveillance of UPEC isolates.
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Affiliation(s)
- Yi Ren
- Department of Immunology, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Educational Ministry of China, School of Basic Medical Sciences, Tianjin Medical UniversityTianjin, China
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd.Shanghai, China
| | - Agata Palusiak
- Department of General Microbiology, Department of Immunobiology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, University of LodzLodz, Poland
| | - Wei Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education – Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai UniversityTianjin, China
| | - Yi Wang
- Department of Immunology, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Educational Ministry of China, School of Basic Medical Sciences, Tianjin Medical UniversityTianjin, China
| | - Xiao Li
- Department of Immunology, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Educational Ministry of China, School of Basic Medical Sciences, Tianjin Medical UniversityTianjin, China
| | - Huiting Wei
- Department of Immunology, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Educational Ministry of China, School of Basic Medical Sciences, Tianjin Medical UniversityTianjin, China
| | - Qingke Kong
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China
| | - Antoni Rozalski
- Department of General Microbiology, Department of Immunobiology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, University of LodzLodz, Poland
| | - Zhi Yao
- Department of Immunology, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Educational Ministry of China, School of Basic Medical Sciences, Tianjin Medical UniversityTianjin, China
| | - Quan Wang
- Department of Immunology, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Educational Ministry of China, School of Basic Medical Sciences, Tianjin Medical UniversityTianjin, China
- State Key Laboratory of Medicinal Chemical Biology, NanKai UniversityTianjin, China
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Tu Q, Zhou X, He Z, Xue K, Wu L, Reich P, Hobbie S, Zhou J. The Diversity and Co-occurrence Patterns of N₂-Fixing Communities in a CO₂-Enriched Grassland Ecosystem. MICROBIAL ECOLOGY 2016; 71:604-615. [PMID: 26280746 DOI: 10.1007/s00248-015-0659-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 08/03/2015] [Indexed: 06/04/2023]
Abstract
Diazotrophs are the major organismal group responsible for atmospheric nitrogen (N2) fixation in natural ecosystems. The extensive diversity and structure of N2-fixing communities in grassland ecosystems and their responses to increasing atmospheric CO2 remain to be further explored. Through pyrosequencing of nifH gene amplicons and extraction of nifH genes from shotgun metagenomes, coupled with co-occurrence ecological network analysis approaches, we comprehensively analyzed the diazotrophic community in a grassland ecosystem exposed to elevated CO2 (eCO2) for 12 years. Long-term eCO2 increased the abundance of nifH genes but did not change the overall nifH diversity and diazotrophic community structure. Taxonomic and phylogenetic analysis of amplified nifH sequences suggested a high diversity of nifH genes in the soil ecosystem, the majority belonging to nifH clusters I and II. Co-occurrence ecological network analysis identified different co-occurrence patterns for different groups of diazotrophs, such as Azospirillum/Actinobacteria, Mesorhizobium/Conexibacter, and Bradyrhizobium/Acidobacteria. This indicated a potential attraction of non-N2-fixers by diazotrophs in the soil ecosystem. Interestingly, more complex co-occurrence patterns were found for free-living diazotrophs than commonly known symbiotic diazotrophs, which is consistent with the physical isolation nature of symbiotic diazotrophs from the environment by root nodules. The study provides novel insights into our understanding of the microbial ecology of soil diazotrophs in natural ecosystems.
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Affiliation(s)
- Qichao Tu
- Department of Marine Sciences, Ocean College, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, 73019, USA
| | - Xishu Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, 73019, USA
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, 410083, China
| | - Zhili He
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, 410083, China
| | - Kai Xue
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, 410083, China
| | - Liyou Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, 410083, China
| | - Peter Reich
- Department of Forest Resources, University of Minnesota, St. Paul, MN, 55455, USA
- Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, 2753, NSW, Australia
| | - Sarah Hobbie
- Department of Forest Resources, University of Minnesota, St. Paul, MN, 55455, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, 73019, USA.
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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Brito AFD, Braconi CT, Weidmann M, Dilcher M, Alves JMP, Gruber A, Zanotto PMDA. The Pangenome of the Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV). Genome Biol Evol 2015; 8:94-108. [PMID: 26615220 PMCID: PMC4758234 DOI: 10.1093/gbe/evv231] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The alphabaculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is the world's most successful viral bioinsecticide. Through the 1980s and 1990s, this virus was extensively used for biological control of populations of Anticarsia gemmatalis (Velvetbean caterpillar) in soybean crops. During this period, genetic studies identified several variable loci in the AgMNPV; however, most of them were not characterized at the sequence level. In this study we report a full genome comparison among 17 wild-type isolates of AgMNPV. We found the pangenome of this virus to contain at least 167 hypothetical genes, 151 of which are shared by all genomes. The gene bro-a that might be involved in host specificity and carrying transporter is absent in some genomes, and new hypothetical genes were observed. Among these genes there is a unique rnf12-like gene, probably implicated in ubiquitination. Events of gene fission and fusion are common, as four genes have been observed as single or split open reading frames. Gains and losses of genomic fragments (from 20 to 900 bp) are observed within tandem repeats, such as in eight direct repeats and four homologous regions. Most AgMNPV genes present low nucleotide diversity, and variable genes are mainly located in a locus known to evolve through homologous recombination. The evolution of AgMNPV is mainly driven by small indels, substitutions, gain and loss of nucleotide stretches or entire coding sequences. These variations may cause relevant phenotypic alterations, which probably affect the infectivity of AgMNPV. This work provides novel information on genomic evolution of the AgMNPV in particular and of baculoviruses in general.
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Affiliation(s)
- Anderson Fernandes de Brito
- Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Carla Torres Braconi
- Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Manfred Weidmann
- Department of Virology, University Medical Center, Göttingen, Germany
| | - Meik Dilcher
- Department of Virology, University Medical Center, Göttingen, Germany
| | - João Marcelo Pereira Alves
- Department of Parasitology, Institute of Biomedical Sciences-ICB II, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Arthur Gruber
- Department of Parasitology, Institute of Biomedical Sciences-ICB II, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Paolo Marinho de Andrade Zanotto
- Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil
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Galpert D, del Río S, Herrera F, Ancede-Gallardo E, Antunes A, Agüero-Chapin G. An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species. BIOMED RESEARCH INTERNATIONAL 2015; 2015:748681. [PMID: 26605337 PMCID: PMC4641943 DOI: 10.1155/2015/748681] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/26/2015] [Accepted: 08/20/2015] [Indexed: 11/17/2022]
Abstract
Orthology detection requires more effective scaling algorithms. In this paper, a set of gene pair features based on similarity measures (alignment scores, sequence length, gene membership to conserved regions, and physicochemical profiles) are combined in a supervised pairwise ortholog detection approach to improve effectiveness considering low ortholog ratios in relation to the possible pairwise comparison between two genomes. In this scenario, big data supervised classifiers managing imbalance between ortholog and nonortholog pair classes allow for an effective scaling solution built from two genomes and extended to other genome pairs. The supervised approach was compared with RBH, RSD, and OMA algorithms by using the following yeast genome pairs: Saccharomyces cerevisiae-Kluyveromyces lactis, Saccharomyces cerevisiae-Candida glabrata, and Saccharomyces cerevisiae-Schizosaccharomyces pombe as benchmark datasets. Because of the large amount of imbalanced data, the building and testing of the supervised model were only possible by using big data supervised classifiers managing imbalance. Evaluation metrics taking low ortholog ratios into account were applied. From the effectiveness perspective, MapReduce Random Oversampling combined with Spark SVM outperformed RBH, RSD, and OMA, probably because of the consideration of gene pair features beyond alignment similarities combined with the advances in big data supervised classification.
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Affiliation(s)
- Deborah Galpert
- Departamento de Ciencias de la Computación, Universidad Central “Marta Abreu” de Las Villas (UCLV), 54830 Santa Clara, Cuba
| | - Sara del Río
- Department of Computer Science and Artificial Intelligence, Research Center on Information and Communications Technology (CITIC-UGR), University of Granada, 18071 Granada, Spain
| | - Francisco Herrera
- Department of Computer Science and Artificial Intelligence, Research Center on Information and Communications Technology (CITIC-UGR), University of Granada, 18071 Granada, Spain
| | - Evys Ancede-Gallardo
- Centro de Bioactivos Químicos, Universidad Central “Marta Abreu” de Las Villas (UCLV), 54830 Santa Clara, Cuba
| | - Agostinho Antunes
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIMAR/CIIMAR), Universidade do Porto, Rua dos Bragas 177, 4050-123 Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Guillermin Agüero-Chapin
- Centro de Bioactivos Químicos, Universidad Central “Marta Abreu” de Las Villas (UCLV), 54830 Santa Clara, Cuba
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIMAR/CIIMAR), Universidade do Porto, Rua dos Bragas 177, 4050-123 Porto, Portugal
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45
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Feldbauer R, Schulz F, Horn M, Rattei T. Prediction of microbial phenotypes based on comparative genomics. BMC Bioinformatics 2015; 16 Suppl 14:S1. [PMID: 26451672 PMCID: PMC4603748 DOI: 10.1186/1471-2105-16-s14-s1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The accessibility of almost complete genome sequences of uncultivable microbial species from metagenomes necessitates computational methods predicting microbial phenotypes solely based on genomic data. Here we investigate how comparative genomics can be utilized for the prediction of microbial phenotypes. The PICA framework facilitates application and comparison of different machine learning techniques for phenotypic trait prediction. We have improved and extended PICA's support vector machine plug-in and suggest its applicability to large-scale genome databases and incomplete genome sequences. We have demonstrated the stability of the predictive power for phenotypic traits, not perturbed by the rapid growth of genome databases. A new software tool facilitates the in-depth analysis of phenotype models, which associate expected and unexpected protein functions with particular traits. Most of the traits can be reliably predicted in only 60-70% complete genomes. We have established a new phenotypic model that predicts intracellular microorganisms. Thereby we could demonstrate that also independently evolved phenotypic traits, characterized by genome reduction, can be reliably predicted based on comparative genomics. Our results suggest that the extended PICA framework can be used to automatically annotate phenotypes in near-complete microbial genome sequences, as generated in large numbers in current metagenomics studies.
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46
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Frasca M, Bassis S, Valentini G. Learning node labels with multi-category Hopfield networks. Neural Comput Appl 2015. [DOI: 10.1007/s00521-015-1965-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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47
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Cai H, Lilburn TG, Hong C, Gu J, Kuang R, Wang Y. Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments. BMC SYSTEMS BIOLOGY 2015; 9 Suppl 4:S1. [PMID: 26100579 PMCID: PMC4474416 DOI: 10.1186/1752-0509-9-s4-s1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Malaria is a major health threat, affecting over 40% of the world's population. The latest report released by the World Health Organization estimated about 207 million cases of malaria infection, and about 627,000 deaths in 2012 alone. During the past decade, new therapeutic targets have been identified and are at various stages of characterization, thanks to the emerging omics-based technologies. However, the mechanism of malaria pathogenesis remains largely unknown. In this paper, we employ a novel neighborhood subnetwork alignment approach to identify network components that are potentially involved in pathogenesis. RESULTS Our module-based subnetwork alignment approach identified 24 functional homologs of pathogenesis-related proteins in the malaria parasite P. falciparum, using the protein-protein interaction networks in Escherichia coli as references. Eighteen out of these 24 proteins are associated with 418 other proteins that are related to DNA replication, transcriptional regulation, translation, signaling, metabolism, cell cycle regulation, as well as cytoadherence and entry to the host. CONCLUSIONS The subnetwork alignments and subsequent protein-protein association network mining predicted a group of malarial proteins that may be involved in parasite development and parasite-host interaction, opening a new systems-level view of parasite pathogenesis and virulence.
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Ufarté L, Potocki-Veronese G, Laville É. Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology. Front Microbiol 2015; 6:563. [PMID: 26097471 PMCID: PMC4456863 DOI: 10.3389/fmicb.2015.00563] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 05/21/2015] [Indexed: 12/30/2022] Open
Abstract
The rapid expansion of new sequencing technologies has enabled large-scale functional exploration of numerous microbial ecosystems, by establishing catalogs of functional genes and by comparing their prevalence in various microbiota. However, sequence similarity does not necessarily reflect functional conservation, since just a few modifications in a gene sequence can have a strong impact on the activity and the specificity of the corresponding enzyme or the recognition for a sensor. Similarly, some microorganisms harbor certain identified functions yet do not have the expected related genes in their genome. Finally, there are simply too many protein families whose function is not yet known, even though they are highly abundant in certain ecosystems. In this context, the discovery of new protein functions, using either sequence-based or activity-based approaches, is of crucial importance for the discovery of new enzymes and for improving the quality of annotation in public databases. This paper lists and explores the latest advances in this field, along with the challenges to be addressed, particularly where microfluidic technologies are concerned.
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Affiliation(s)
- Lisa Ufarté
- Université de Toulouse, Institut National des Sciences Appliquées (INSA), Université Paul Sabatier (UPS), Institut National Polytechnique (INP), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP) , Toulouse, France ; INRA - UMR792 Ingénierie des Systèmes Biologiques et des Procédés , Toulouse, France ; CNRS, UMR5504 , Toulouse, France
| | - Gabrielle Potocki-Veronese
- Université de Toulouse, Institut National des Sciences Appliquées (INSA), Université Paul Sabatier (UPS), Institut National Polytechnique (INP), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP) , Toulouse, France ; INRA - UMR792 Ingénierie des Systèmes Biologiques et des Procédés , Toulouse, France ; CNRS, UMR5504 , Toulouse, France
| | - Élisabeth Laville
- Université de Toulouse, Institut National des Sciences Appliquées (INSA), Université Paul Sabatier (UPS), Institut National Polytechnique (INP), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP) , Toulouse, France ; INRA - UMR792 Ingénierie des Systèmes Biologiques et des Procédés , Toulouse, France ; CNRS, UMR5504 , Toulouse, France
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Cheng Y, Perocchi F. ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling. Nucleic Acids Res 2015; 43:W160-8. [PMID: 25956654 PMCID: PMC4489284 DOI: 10.1093/nar/gkv455] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/24/2015] [Indexed: 01/17/2023] Open
Abstract
ProtPhylo is a web-based tool to identify proteins that are functionally linked to either a phenotype or a protein of interest based on co-evolution. ProtPhylo infers functional associations by comparing protein phylogenetic profiles (co-occurrence patterns of orthology relationships) for more than 9.7 million non-redundant protein sequences from all three domains of life. Users can query any of 2048 fully sequenced organisms, including 1678 bacteria, 255 eukaryotes and 115 archaea. In addition, they can tailor ProtPhylo to a particular kind of biological question by choosing among four main orthology inference methods based either on pair-wise sequence comparisons (One-way Best Hits and Best Reciprocal Hits) or clustering of orthologous proteins across multiple species (OrthoMCL and eggNOG). Next, ProtPhylo ranks phylogenetic neighbors of query proteins or phenotypic properties using the Hamming distance as a measure of similarity between pairs of phylogenetic profiles. Candidate hits can be easily and flexibly prioritized by complementary clues on subcellular localization, known protein–protein interactions, membrane spanning regions and protein domains. The resulting protein list can be quickly exported into a csv text file for further analyses. ProtPhylo is freely available at http://www.protphylo.org.
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Affiliation(s)
- Yiming Cheng
- Gene Center, Ludwig-Maximilians-University, Munich, Bavaria 81377, Germany Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Bavaria 85764, Germany
| | - Fabiana Perocchi
- Gene Center, Ludwig-Maximilians-University, Munich, Bavaria 81377, Germany Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Bavaria 85764, Germany
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50
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Insights from the metagenome of an acid salt lake: the role of biology in an extreme depositional environment. PLoS One 2015; 10:e0122869. [PMID: 25923206 PMCID: PMC4414474 DOI: 10.1371/journal.pone.0122869] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/24/2015] [Indexed: 12/31/2022] Open
Abstract
The extremely acidic brine lakes of the Yilgarn Craton of Western Australia are home to some of the most biologically challenging waters on Earth. In this study, we employed metagenomic shotgun sequencing to generate a microbial profile of the depositional environment associated with the sulfur-rich sediments of one such lake. Of the 1.5 M high-quality reads generated, 0.25 M were mapped to protein features, which in turn provide new insights into the metabolic function of this community. In particular, 45 diverse genes associated with sulfur metabolism were identified, the majority of which were linked to either the conversion of sulfate to adenylylsulfate and the subsequent production of sulfide from sulfite or the oxidation of sulfide, elemental sulfur, and thiosulfate via the sulfur oxidation (Sox) system. This is the first metagenomic study of an acidic, hypersaline depositional environment, and we present evidence for a surprisingly high level of microbial diversity. Our findings also illuminate the possibility that we may be meaningfully underestimating the effects of biology on the chemistry of these sulfur-rich sediments, thereby influencing our understanding of past geobiological conditions that may have been present on Earth as well as early Mars.
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