1
|
Lv JX, Liu X, Pei YY, Song ZG, Chen X, Hu SJ, She JL, Liu Y, Chen YM, Zhang YZ. Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak. Virus Evol 2024; 10:veae020. [PMID: 38562953 PMCID: PMC10984623 DOI: 10.1093/ve/veae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/24/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Despite extensive scientific efforts directed toward the evolutionary trajectory of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans at the beginning of the COVID-19 epidemic, it remains unclear how the virus jumped into and evolved in humans so far. Herein, we recruited almost all adult coronavirus disease 2019 (COVID-19) cases appeared locally or imported from abroad during the first 8 months of the outbreak in Shanghai. From these patients, SARS-CoV-2 genomes occupying the important phylogenetic positions in the virus phylogeny were recovered. Phylogenetic and mutational landscape analyses of viral genomes recovered here and those collected in and outside of China revealed that all known SARS-CoV-2 variants exhibited the evolutionary continuity despite the co-circulation of multiple lineages during the early period of the epidemic. Various mutations have driven the rapid SARS-CoV-2 diversification, and some of them favor its better adaptation and circulation in humans, which may have determined the waxing and waning of various lineages.
Collapse
Affiliation(s)
- Jia-Xin Lv
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Xiang Liu
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yuan-Yuan Pei
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
- Shanghai Public Health Clinical Center, No. 2901 Canglang Road, Jinshan District, Shanghai 210508, China
| | - Zhi-Gang Song
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
- Shanghai Public Health Clinical Center, No. 2901 Canglang Road, Jinshan District, Shanghai 210508, China
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou, Guangdong 510642, China
| | - Shu-Jian Hu
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Jia-Lei She
- Shanghai Public Health Clinical Center, No. 2901 Canglang Road, Jinshan District, Shanghai 210508, China
| | - Yi Liu
- Shanghai Public Health Clinical Center, No. 2901 Canglang Road, Jinshan District, Shanghai 210508, China
| | - Yan-Mei Chen
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yong-Zhen Zhang
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| |
Collapse
|
2
|
Chen C, Wang C, Pang R, Liu H, Yin W, Chen J, Tao L. Comprehensive single-cell transcriptomic and proteomic analysis reveals NK cell exhaustion and unique tumor cell evolutionary trajectory in non-keratinizing nasopharyngeal carcinoma. J Transl Med 2023; 21:278. [PMID: 37098551 PMCID: PMC10127506 DOI: 10.1186/s12967-023-04112-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/08/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Nonkeratinizing nasopharyngeal carcinoma (NK-NPC) has a strong association with Epstein-Barr virus (EBV) infection. The role of NK cells and the tumor cell evolutionary trajectory in NK-NPC remain unclear. In this study, we aim to investigate the function of NK cell and the evolutionary trajectory of tumor cells in NK-NPC by single-cell transcriptomic analysis, proteomics and immunohistochemistry. METHODS NK-NPC (n = 3) and normal nasopharyngeal mucosa cases (n = 3) were collected for proteomic analysis. Single-cell transcriptomic data of NK-NPC (n = 10) and nasopharyngeal lymphatic hyperplasia (NLH, n = 3) were obtained from Gene Expression Omnibus (GSE162025 and GSE150825). Quality control, dimension reduction and clustering were based on Seurat software (v4.0.2) process and batch effects were removed by harmony (v0.1.1) software. Normal cells of nasopharyngeal mucosa and tumor cells of NK-NPC were identified using copykat software (v1.0.8). Cell-cell interactions were explored using CellChat software (v1.4.0). Tumor cell evolutionary trajectory analysis was performed using SCORPIUS software (v1.0.8). Protein and gene function enrichment analyses were performed using clusterProfiler software (v4.2.2). RESULTS A total of 161 differentially expressed proteins were obtained between NK-NPC (n = 3) and normal nasopharyngeal mucosa (n = 3) by proteomics (log2 fold change > 0.5 and P value < 0.05). Most of proteins associated with the nature killer cell mediated cytotoxicity pathway were downregulated in the NK-NPC group. In single cell transcriptomics, we identified three NK cell subsets (NK1-3), among which NK cell exhaustion was identified in the NK3 subset with high ZNF683 expression (a signature of tissue-resident NK cell) in NK-NPC. We demonstrated the presence of this ZNF683 + NK cell subset in NK-NPC but not in NLH. We also performed immunohistochemical experiments with TIGIT and LAG3 to confirm NK cell exhaustion in NK-NPC. Moreover, the trajectory analysis revealed that the evolutionary trajectory of NK-NPC tumor cells was associated with the status of EBV infection (active or latent). The analysis of cell-cell interactions uncovered a complex network of cellular interactions in NK-NPC. CONCLUSIONS This study revealed that the NK cell exhaustion might be induced by upregulation of inhibitory receptors on the surface of NK cells in NK-NPC. Treatments for the reversal of NK cell exhaustion may be a promising strategy for NK-NPC. Meanwhile, we identified a unique evolutionary trajectory of tumor cells with active status of EBV-infection in NK-NPC for the first time. Our study may provide new immunotherapeutic targets and new sight of evolutionary trajectory involving tumor genesis, development and metastasis in NK-NPC.
Collapse
Affiliation(s)
- Cuimin Chen
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Chun Wang
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Ruifang Pang
- Department of Precision Research Institute, Peking University Shenzhen Hospital, Shenzhen, China
| | - Huanyu Liu
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Weihua Yin
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jiakang Chen
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, China.
| | - Lili Tao
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, China.
| |
Collapse
|
3
|
Song M, Xie H, Liu W, Zhao M, Deng Z, Zhang L, Liu H, Huang Y, Li H, Ren Y, Chen C. Characterization of the evolution trajectory and immune profiling of new histologic patterns in lung adenocarcinoma. J Gene Med 2022; 24:e3455. [PMID: 36194517 DOI: 10.1002/jgm.3455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/08/2022] Open
Abstract
In lung adenocarcinoma, the appearance of morphologically diverse tumor regions, termed histological patterns are closely associated with disease progression and lymph node metastasis. However, the molecular characteristics of the histological patterns in lung adenocarcinoma and the underlying molecular evolutionary mechanisms between the histological patterns in primary tumors and lymph node metastases are poorly understood. Here we re-analyzed the large TCGA lung adenocarcinoma dataset and depicted a comprehensive profiling of the genome and transcriptome across the histological patterns in lung adenocarcinoma. Tumor phylogenetic trajectory analysis suggested that the complex glands is more apt to metastasize to the lymph node. Further deconvolution of the tumor microenvironment demonstrated that the complex glands had a higher infiltration of cancer-associated fibroblasts (CAFs). Single-cell transcriptome profiling of complex glands pattern identified a novel CAF subtype co-expressing fibroblast activation protein-alpha (FAP) and stimulator of interferon genes (STING). Moreover, our data demonstrated that FAP is an important downstream effector of STING in CAFs. In summary, our results aimed to provide the basis for the development of innovative therapeutic guidelines and intervention strategies for LUAD patients.
Collapse
Affiliation(s)
- Minfang Song
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Huikang Xie
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Liu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Mengmeng Zhao
- Research Center of Translational Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | | | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Haipeng Liu
- Central Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | | | - Hanjie Li
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yijiu Ren
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| |
Collapse
|
4
|
Ma Q, Wang J, Qi J, Peng D, Guan B, Zhang J, Li Z, Zhang H, Li T, Shi Y, Li X, Zhou L, Chen K, Ci W. Increased chromosomal instability characterizes metastatic renal cell carcinoma. Transl Oncol 2020; 14:100929. [PMID: 33157517 PMCID: PMC7649528 DOI: 10.1016/j.tranon.2020.100929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/16/2022] Open
Abstract
The clonal origin and parallel evolution of the metastatic lesions and primary tumour. The evolutionary branches of primary and metastatic clones diverge early in the development of the tumour. Increased genome instability and specific enriched somatic copy number alteration (SCNAs) in metastatic lesions compared to primary tumour. LOH at 14q, loss of 14q32.31 and gain of 6p22.2 are highly selected events during metastatic evolution.
The evolutionary trajectories of treatment-naïve metastatic tumour are largely unknown. Such knowledge is crucial for cancer prevention and therapeutic interventions. Herein, we performed whole genome or exome sequencing of 19 tumour specimens and 8 matched normal kidney tissues from 8 clear cell renal cell carcinoma (ccRCC) patients. The clonal origin and parallel evolution of the metastatic lesions and primary tumour is identified in all 8 patients. But the evolutionary branches of primary and metastatic clones diverge early in the development of the tumour. More importantly, larger scale genomic aberrations including somatic copy number alteration (SCNA) or loss of heterozygosity (LOH) differentiate the metastasis lesions from primary tumour. Based on it, we identify that LOH at 14q, loss of 14q32.31 and gain of 6p22.2 are highly selected events during metastatic evolution. Further functional validations of multiple genes within the SCNA regions indicated that these selected events interact to drive metastatic risk with potential therapeutic relevance. Collectively, we described increased genome instability in metastatic ccRCC and validated it via molecular biology, providing an evolution pattern which may facilitate the translation of basic finding.
Collapse
Affiliation(s)
- Qin Ma
- Department of Urology, Peking University First Hospital, Beijing 100034, China; Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jilu Wang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Qi
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ding Peng
- Department of Urology, Peking University First Hospital, Beijing 100034, China; Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bao Guan
- Department of Urology, Peking University First Hospital, Beijing 100034, China; Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Institute of Urology, Peking University, Beijing 100034, China; National Urological Cancer Centre, Beijing 100034, China
| | - Jianye Zhang
- Department of Urology, Peking University First Hospital, Beijing 100034, China; Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Institute of Urology, Peking University, Beijing 100034, China; National Urological Cancer Centre, Beijing 100034, China
| | - Zhongwu Li
- Department of Pathology, Peking University School of Oncology, 100142 Beijing, China
| | - Hongxian Zhang
- Department of Urology, School of Life Sciences, Third Hospital, Peking University, Beijing 100083, China
| | - Ting Li
- Department of Urology, Peking University First Hospital, Beijing 100034, China; Institute of Urology, Peking University, Beijing 100034, China; National Urological Cancer Centre, Beijing 100034, China
| | - Yue Shi
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing 100034, China; Institute of Urology, Peking University, Beijing 100034, China; National Urological Cancer Centre, Beijing 100034, China.
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing 100034, China; Institute of Urology, Peking University, Beijing 100034, China; National Urological Cancer Centre, Beijing 100034, China.
| | - Ke Chen
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Weimin Ci
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
5
|
Colangelo P, Ventura D, Piras P, Pagani Guazzugli Bonaiuti J, Ardizzone G. Are developmental shifts the main driver of phenotypic evolution in Diplodus spp. (Perciformes: Sparidae)? BMC Evol Biol 2019; 19:106. [PMID: 31113358 PMCID: PMC6528360 DOI: 10.1186/s12862-019-1424-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 04/17/2019] [Indexed: 11/14/2022] Open
Abstract
Background Sparid fishes of the genus Diplodus show a complex life history. Juveniles have adaptations well suited to life in the water column. When fishes recruit into the adult population, individuals develop a radically differentiated shape that reflects their adaptation to the new benthic environment typical of the adult. A comparative analysis of ontogenetic trajectories was performed to assess the presence of divergence in the developmental pattern. By using a geometric morphometric approach, we investigated the pattern of shape variation across ontogenetic stages that span from early settlement to the adult stage in four species of the genus Diplodus. Landmarks were collected on the whole body of fishes to quantify the phenotypic variation along two well defined life stages, i.e. juvenile and adult. A comparative analysis of ontogenetic trajectories was performed to assess the presence of divergence in the developmental pattern. Subsequently, we investigated the patterns of integration and modularity as proxy for the alteration of the developmental processes. This have allowed to give an insight in morphological developmental patterns across ecologically and ontogenetically differentiated life stages and to investigate the process leading to the adult shape. Result Our results suggest that the origin of morphological novelties in Diplodus spp. arise from shifts of the ontogenetic trajectories during development. During the settlement phase, the juveniles’ morphological shapes converge towards similar regions of the morphospace. When the four species approach the transition between settlement and recruitment, we observe the lowest level of inter- and intra-specific disparity. After this transition we detect an abrupt shift of ontogenetic trajectories, i.e. the path taken by species during development, that led to highly divergent adult phenotypes. Discussion We suggest that the evolution of new ecomorphologies, better suited to exploit different niches (pelagic vs. benthonic) and reduce inter-specific competition in Diplodus spp., are related to the shift in the ontogenetic trajectory that in turn is associated to changes in modularity and integration pattern. Electronic supplementary material The online version of this article (10.1186/s12862-019-1424-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Paolo Colangelo
- Research Institute on Terrestrial Ecosystems, National Research Council, Via Salaria km 29.300, 00015, Monterotondo, Rome, Italy. .,Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Via Borelli 50, 00161, Rome, Italy.
| | - Daniele Ventura
- Department of Environmental Biology, Sapienza University, Rome, Italy
| | - Paolo Piras
- Department of Cardiovascular Respiratory Nephrologic and Geriatric Sciences, Sapienza University, Rome, Italy
| | | | | |
Collapse
|
6
|
Xiang L, Liu C, Luo J, He L, Deng Y, Yuan J, Wu C, Cai Y. A tuber mustard AP2/ERF transcription factor gene, BjABR1, functioning in abscisic acid and abiotic stress responses, and evolutionary trajectory of the ABR1 homologous genes in Brassica species. PeerJ 2018; 6:e6071. [PMID: 30581669 PMCID: PMC6294115 DOI: 10.7717/peerj.6071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/02/2018] [Indexed: 01/05/2023] Open
Abstract
The AP2/ERF superfamily of transcription factors is one of the largest transcription factor families in plants and plays an important role in plant development processes and stress responses. In this study, BjABR1, an AP2/ERF superfamily gene, from tuber mustard (Brassica juncea var. tumida Tsen et Lee), sharing high amino acid sequence similarity with the AtABR1 (Arabidopsis thaliana AP2-like abscisic acid repressor 1) gene, were performed functional research, and the ABR1 homologous genes in Brassica species were identified and performed phylogenetic analysis. The promoter sequence of BjABR1 contained many phytohormone- and stress-related cis-elements; ABA (abscisic acid) and abiotic stresses can induce BjABR1 expression in tuber mustard; overexpression of BjABR1 in Arabidopsis can alleviate plant sensitivity to ABA and salt and osmotic stresses, and the alleviation may be due to changes in stress/ABA-induced gene expression. These results indicated that BjABR1 functions in ABA and abiotic stress responses. By BLAST searches against the genome database of five Brassica species (three diploids, B. rapa, B. nigra, and B. oleracea, and two allotetraploid, B. juncea and B. napus) using the protein sequence of AtABR1, 3, 3, 3, 6, and 5 ABR1 homologous genes in B. nigra, B. rapa, B. oleracea, B. juncea, and B. napus were identified, respectively, and they shared high sequence similarity. By sequence analysis, annotation mistakes of the protein-coding regions of two ABR1 homologous genes, GSBRNA2T00134741001 and BjuB007684, were found and corrected. Then, the evolution analysis of these ABR1 homologous genes showed that the ancestor of the three diploid species had three ABR1 homologous genes and each diploid inherited all the three genes from their ancestor; then, allotetraploid B. juncea inherited all the six genes from B. rapa and B. nigra with no gene lost, while allotetraploid B. napus inherited all the three genes from B. oleracea and two genes from B. rapa with one gene lost, indicating that ABR1 homologous genes possessed greater hereditary conservation in Brassica species. The ABR1 homologous genes between B. rapa and B. oleracea shared much higher sequence similarity compared to that of B. nigra in diploid species, indicating that ABR1 homologous genes in B. nigra had experienced more rapid evolution, and B. rapa and B. oleracea may share closer relationship compared to B. nigra. Moreover, the spatial and temporal expression analysis of six ABR1 homologous genes of tuber mustard showed that they possessed different expression models. These results imply that ABR1 homologous genes are important to Brassica plants, and they may possess similar function in ABA and abiotic stress responses but play a role in different tissues and growing stages of plant. This study will provide the foundation to the functional research of ABR1 homologous genes in the Brassica species and help to reveal and understand the evolution mechanisms of Brassica species.
Collapse
Affiliation(s)
- Liuxin Xiang
- Chongqing University of Posts and Telecommunications, Chongqing Key Laboratory on Big Data for Bio Intelligence, School of Bioinformatics, School of Software Engineering, Chongqing, China
| | - Chao Liu
- Chongqing University of Posts and Telecommunications, Chongqing Key Laboratory on Big Data for Bio Intelligence, School of Bioinformatics, School of Software Engineering, Chongqing, China
| | - Jingzhi Luo
- Chongqing University of Posts and Telecommunications, Chongqing Key Laboratory on Big Data for Bio Intelligence, School of Bioinformatics, School of Software Engineering, Chongqing, China
| | - Lin He
- Chongqing University of Posts and Telecommunications, Chongqing Key Laboratory on Big Data for Bio Intelligence, School of Bioinformatics, School of Software Engineering, Chongqing, China
| | - Yushan Deng
- Chongqing University of Posts and Telecommunications, Chongqing Key Laboratory on Big Data for Bio Intelligence, School of Bioinformatics, School of Software Engineering, Chongqing, China
| | - Jie Yuan
- Chongqing University of Posts and Telecommunications, Chongqing Key Laboratory on Big Data for Bio Intelligence, School of Bioinformatics, School of Software Engineering, Chongqing, China
| | - Chaofeng Wu
- Chongqing University of Posts and Telecommunications, Chongqing Key Laboratory on Big Data for Bio Intelligence, School of Bioinformatics, School of Software Engineering, Chongqing, China
| | - Yingfan Cai
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Kaifeng, Henan, China
| |
Collapse
|
7
|
Song X, Ma X, Li C, Hu J, Yang Q, Wang T, Wang L, Wang J, Guo D, Ge W, Wang Z, Li M, Wang Q, Ren T, Feng S, Wang L, Zhang W, Wang X. Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species. BMC Genomics 2018; 19:346. [PMID: 29743014 PMCID: PMC5944053 DOI: 10.1186/s12864-018-4744-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 04/30/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The BES1 gene family, an important class of plant-specific transcription factors, play key roles in the BR signal pathway in plants, regulating various development processes. Until now, there has been no comprehensive analysis of the BES1 gene family in Brassica napus, and a cross-genome exploration of their origin, copy number changes, and functional innovation in plants was also not available. RESULTS We identified 28 BES1 genes in B. napus from its two subgenomes (AA and CC). We found that 71.43% of them were duplicated in the tetraploidization, and their gene expression showed a prominent subgenome bias in the roots. Additionally, we identified 104 BES1 genes in another 18 representative angiosperms and performed a comparative analysis with B. napus, including evolutionary trajectory, gene duplication, positive selection, and expression pattern. Exploiting the available genome datasets, we performed a large-scale analysis across plants and algae suggested that the BES1 gene family could have originated from group F, expanding to form other groups (A to E) by duplicating or alternatively deleting some domains. We detected an additional domain containing M4 to M8 in exclusively groups F1 and F2. We found evidence that whole-genome duplication (WGD) contributed the most to the expansion of this gene family among examined dicots, while dispersed duplication contributed the most to expansion in certain monocots. Moreover, we inferred that positive selection might have occurred on major phylogenetic nodes during the evolution of plants. CONCLUSIONS Grossly, a cross-genome comparative analysis of the BES1 genes in B. napus and other species sheds light on understanding its copy number expansion, natural selection, and functional innovation.
Collapse
Affiliation(s)
- Xiaoming Song
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Xiao Ma
- Library, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Chunjin Li
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Jingjing Hu
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Qihang Yang
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Tong Wang
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Li Wang
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Jinpeng Wang
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Di Guo
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Weina Ge
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Zhenyi Wang
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Miaomiao Li
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Qiumei Wang
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Tianzeng Ren
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Shuyan Feng
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Lixia Wang
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Weimeng Zhang
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| | - Xiyin Wang
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, 063210 Hebei China
| |
Collapse
|
8
|
James LA. Arrested geomorphic trajectories and the long-term hidden potential for change. J Environ Manage 2017; 202:412-423. [PMID: 28214027 DOI: 10.1016/j.jenvman.2017.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 02/01/2017] [Accepted: 02/06/2017] [Indexed: 06/06/2023]
Abstract
Geomorphic systems often experience morphological changes that define a trajectory over decadal time periods. These trends can be halted by natural inhibitors such as vegetation, knickpoints, bed armor, or bank cohesion, or by anthropogenic inhibitors such as revetment, levees, or dams. Details about where and how channels and floodplains are stabilized are often poorly understood, which poses a risk that modern projects could unwittingly remove critical stabilizing elements (inhibitors) and unleash an episode of rapid change. The potential for destabilization is particularly keen for rivers that were severely altered by human activities but were stabilized by an inhibitor before readjustment was complete. This study uses aerial photographs to examine two cases of arrested geomorphic trajectories in the lower Yuba and Feather Rivers of northern California after 150 years of severe human disturbance. Channel adjustments were inhibited in distinctly different ways. First, channelization of the Feather River across a high-amplitude meander bend ∼4 km below the Yuba-Feather River confluence resulted in a knickpoint at Shanghai Shoals that retreated upstream at an average rate of 3.67 m/yr from 1963 to 2013 with two episodes of rapid retreat. Shanghai Shoals was breached in 2013. Second, numerous wing dams on the Yuba River constructed in the early nineteenth century limit floodplain widening and prevent return to an anastomosing channel planform. Their stabilizing role is important to preventing mobilization of mining sediment with high concentrations of mercury. These rivers exemplify how arrested geomorphic trajectories may impact sustainable river management, and how recognition of fluvial evolution is essential to sustainable river management.
Collapse
|
9
|
Pal A, Tripathi A. An in silico approach to elucidate structure based functional evolution of oxacillinase. Comput Biol Chem 2016; 64:145-153. [PMID: 27343874 DOI: 10.1016/j.compbiolchem.2016.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 05/25/2016] [Accepted: 06/06/2016] [Indexed: 11/25/2022]
Abstract
Bacterial Oxacillinases (OXAs), genetically being extremely diverse and highly versatile in hydrolyzing antibiotics of different classes, holds utmost significant clinical importance. Hence, to analyze functional evolution of this enzyme, plausible changes in drug profile, affinity and binding stability of different subclasses of OXA with their preferred drugs, viz. penicillin, ceftazidime, imipenem/meropenem were investigated. Maximum-Likelihood dendrogram was constructed and based on tree topology, the least and most divergent variants of each clade were selected. Pocket characterization, enzyme structural stability and mutational effect were analyzed in silico. Modes of interaction of selected OXA variants with respective antibiotics were analyzed by Autodock4.0 and LIGPLOT. Comparative mobility profiling and subsequent ΔG° and Km calculations of representative OXA variants revealed that after RSBL evolution, perhaps, two competitive strategies evolved among the OXA variants. Either loops flanking helix5 gets stabilized or it becomes more flexible. Therefore, while OXA variants (e.g. OXA-2, OXA-32, OXA-23, OXA-133, OXA-24, OXA-25, OXA-51 and OXA-75) with highly stabilized loops flanking helix5 exhibited improved binding stability and affinity towards carbapenems, especially meropenem, OXA variants (e.g. OXA-10, OXA-251, OXA-48 and OXA-247) possessing highly flexibile loops flanking helix5 revealed their catalytic proficiency towards ceftazidime. Moreover, LIGPLOT and PROMALS3D jointly identified ten consensuses/conserved residues, viz. P68, A69, F72, K73, W105, V120, W164, L169, K216 and G218 to be critical for drug hydrolysis. Hence, novel inhibitors could be designed to target these sites.
Collapse
Affiliation(s)
- Arijit Pal
- Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, 108 C.R. Avenue, Kolkata 700073, India
| | - Anusri Tripathi
- Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, 108 C.R. Avenue, Kolkata 700073, India.
| |
Collapse
|
10
|
Abstract
Background Phenotypic transitions, such as trait gain or loss, are predicted to carry evolutionary consequences for the genes that control their development. For example, trait losses can result in molecular decay of the pathways underlying the trait. Focusing on the Iochrominae clade (Solanaceae), we examine how repeated losses of floral anthocyanin pigmentation associated with flower color transitions have affected the molecular evolution of three anthocyanin pathway genes (Chi, F3h, and Dfr). Results We recovered intact coding regions for the three genes in all of the lineages that have lost floral pigmentation, suggesting that molecular decay is not associated with these flower color transitions. However, two of the three genes (Chi, F3h) show significantly elevated dN/dS ratios in lineages without floral pigmentation. Maximum likelihood analyses suggest that this increase is due to relaxed constraint on anthocyanin genes in the unpigmented lineages as opposed to positive selection. Despite the increase, the values for dN/dS in both pigmented and unpigmented lineages were consistent overall with purifying selection acting on these loci. Conclusions The broad conservation of anthocyanin pathway genes across lineages with and without floral anthocyanins is consistent with the growing consensus that losses of pigmentation are largely achieved by changes in gene expression as opposed to structural mutations. Moreover, this conservation maintains the potential for regain of flower color, and indicates that evolutionary losses of floral pigmentation may be readily reversible. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0675-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Winnie W Ho
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA.
| |
Collapse
|
11
|
Pal A, Tripathi A. An in silico approach for understanding the molecular evolution of clinically important metallo-beta-lactamases. Infect Genet Evol 2013; 20:39-47. [PMID: 23954421 DOI: 10.1016/j.meegid.2013.07.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 06/20/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
Abstract
Resistance to carbapenem, considered to be the drug of last resort for treating serious enterobacterial infections, is a growing problem. Metallo-beta-lactamase (MBL) mediated carbapenem resistance is considered to be clinically most important, since no traditional inhibitors work against them. Hence, we have investigated the changes in drug profile, affinity and binding stability of meropenem with clinically important MBLs viz., IMP, VIM and NDM during the course of molecular evolution. Phylogenetic trees were constructed and amino acids positions, presumed to be exposed to positive selection pressure were analyzed. Based on sequence diversity and selection pressure, IMP-1, IMP-8, IMP-9, IMP-21, IMP-27, IMP-20 and IMP-26 among IMP genes; VIM-1, VIM-2, VIM-13, VIM-29, VIM-18 and VIM-7 among VIM genes and NDM-1 had been selected for in silico analysis. Mode of interaction of selected MBL variants with meropenem were analyzed by Autodock4.0 and LIGPLOT analysis. In all the trajectories, we had found an increase in mouth opening/solvent accessible volume/area of the catalytic pocket and decrease in Gibbs' free energy (ΔG°) for binding with meropenem and Michealis-Menten constant (Km) - indicating an increase in choice of drugs, binding stability and meropenem affinity from primitive to advanced MBL variants, with exceptions of IMP-20, IMP-26, VIM-13 and VIM-18 which might be due to sign epistasis. Intergenic comparison revealed NDM-1 might have greater drug profile and catalytic efficiency than IMP-1 and VIM-2 due to largest pocket opening and least distance between the Zn-I ion and β-lactam oxygen of meropenem.
Collapse
Affiliation(s)
- Arijit Pal
- Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, 108, C.R. Avenue, Kolkata 700 073, India.
| | | |
Collapse
|