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Classification of protein motifs based on subcellular localization uncovers evolutionary relationships at both sequence and functional levels

Marcos Parras-Moltó, Francisco J Campos-Laborie, Juan García-Diéguez, M Rodríguez-Griñolo, Antonio J Pérez-Pulido
2013 BMC Bioinformatics  
On the other hand, motifs define amino acid arrangements conserved between protein family members and represent powerful tools for assigning function to protein sequences.  ...  The ideal motif would identify all members of a protein family but in practice many motifs identify both family members and unrelated proteins, referred to as True Positive (TP) and False Positive (FP)  ...  We also acknowledge institutional support from the Junta de Andalucía to the CABD, and to the Unit of Information Resources for Research at the "Consejo Superior de Investigaciones Científicas" (CSIC)  ... 
doi:10.1186/1471-2105-14-229 pmid:23865897 pmcid:PMC3724711 fatcat:opbkog2wsfamfguvcudt3n3kvy

Genome-Wide Identification and Transcriptional Analysis of Arabidopsis DUF506 Gene Family

Sheng Ying
2021 International Journal of Molecular Sciences  
Phylogenetic modeling classified three groups of plant DUF506 genes that suggested functional preservation among the groups based on conserved gene structure and motifs.  ...  Subcellular protein localization analysis revealed that DUF506 proteins were present in different organelles.  ...  Acknowledgments: The author thanks Sylvia Warner (Noble Research Institute) for lab assistance, Wolf Scheible (Noble Research Institute) and Elison Blancaflor (NASA) for critical comments of the manuscript  ... 
doi:10.3390/ijms222111442 pmid:34768874 pmcid:PMC8583954 fatcat:hfvjd5topjbulj36hpme4hu7fu

Comparative Analysis, Characterization and Evolutionary Study of Dirigent Gene Family in Cucurbitaceae and Expression of Novel Dirigent Peptide against Powdery Mildew Stress

Vivek Yadav, Zhongyuan Wang, Xiaozhen Yang, Chunhua Wei, Xuan Changqing, Xian Zhang
2021 Genes  
In summary, based on the expression and in-silico analysis, we propose a role of DIRs in disease resistance mechanisms.  ...  Dirigent (DIR) proteins are induced under various stress conditions and involved in sterio- and regio-selective coupling of monolignol.  ...  Acknowledgments: The authors wish to acknowledge the financial support of the NWAFU Yangling and of the College of Horticulture.  ... 
doi:10.3390/genes12030326 pmid:33668231 pmcid:PMC7996225 fatcat:tsycrs2hcrev5oifp7iwh3jxga

Bridging protein local structures and protein functions

Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen
2008 Amino Acids  
One of the major goals of molecular and evolutionary biology is to understand the functions of proteins by extracting functional information from protein sequences, structures and interactions.  ...  In particular, we emphasize the newly developed structure-based methods, which are able to identify locally structural motifs and reveal their relationship with protein functions.  ...  Acknowledgments This work was supported by the National Natural Science Foundation of China (NSFC) under Grant No. 10631070 and No. 60503004.  ... 
doi:10.1007/s00726-008-0088-8 pmid:18421562 fatcat:micrifjcrfetnafnm4fx45ouom

Identification and Expression Profiling of the Auxin Response Factors in Dendrobium officinale under Abiotic Stresses

Zhehao Chen, Ye Yuan, Di Fu, Chenjia Shen, Yanjun Yang
2017 International Journal of Molecular Sciences  
Based on our data, several hormones and significant stress responsive DnARF genes have been identified.  ...  To uncover the basic information of DnARF gene responses to abiotic stresses, we analyzed their expression patterns under various hormones and abiotic treatments.  ...  (b) Classification of DnARF proteins based on their amino acid preferences and domain structures.  ... 
doi:10.3390/ijms18050927 pmid:28471373 pmcid:PMC5454840 fatcat:d43ka22up5cerdpj4jmhyc4wxm

Uses of Phage Display in Agriculture: Sequence Analysis and Comparative Modeling of Late Embryogenesis Abundant Client Proteins Suggest Protein-Nucleic Acid Binding Functionality

Rekha Kushwaha, A. Bruce Downie, Christina M. Payne
2013 Computational and Mathematical Methods in Medicine  
Our methods uncover what appears to be a predilection for protein-nucleic acid interactions among LEA client proteins, which is suggestive of subcellular residence.  ...  Here, we use sequence analysis and homology modeling of the client proteins to ascertain common sequence and structural properties that may contribute to binding affinity with the protective LEA protein  ...  For both patterns, PDBeMotif suggests-based on existing 3D structural data of proteins containing these sequence patterns-that glycerophosphate, ribose, and deoxyribose are among the structure-bound ligands  ... 
doi:10.1155/2013/470390 pmid:23956788 pmcid:PMC3727180 fatcat:hgje6okbwjhixaadtmh2krnzma

Genome-wide identification and analysis of WRKY gene family in maize provide insights into regulatory network in response to abiotic stresses

Wenjing Hu, Qiaoyu Ren, Yali Chen, Guoliang Xu, Yexiong Qian
2021 BMC Plant Biology  
Further, subcellular localization prediction, functional annotation and interaction analysis of ZmWRKY proteins were also performed to predict their interactions and associations involved in potential  ...  On the basis of features of molecular structure and a comparison of phylogenetic relationships of WRKY transcription factor families from Arabidopsis, rice and maize, all 140 ZmWRKY proteins in maize were  ...  Funding This study was supported by grants from the National Natural Science We confirm that all experimental protocols were approved by Anhui Agriculture University and Anhui Normal University.  ... 
doi:10.1186/s12870-021-03206-z pmid:34544366 fatcat:yniv3st4vbhollw6zplnf64zl4

Understanding Diversity, Evolution, and Structure of Small Heat Shock Proteins in Annelida Through in Silico Analyses

Mercedes de la Fuente, Marta Novo
2022 Frontiers in Physiology  
Our results support an evolutionary history of these proteins based on duplication events prior to the Spiralia split. Monomeric sHsps 76) were further divided into five subclusters.  ...  These proteins are localized in different subcellular compartments and play critical roles in the stress physiology of tissues, organs, and whole multicellular eukaryotes.  ...  Analyses of a wide range of proteomes (Kiraga et al., 2007) indicated that the isoelectric point of proteins show clear relationships with the length of proteins, their subcellular localization, and  ... 
doi:10.3389/fphys.2022.817272 pmid:35530508 pmcid:PMC9075518 fatcat:cckc55plknbfvim7c2iixaamvy

Functional classification of long non-coding RNAs by k-mer content

Jessime M. Kirk, Susan O. Kim, Kaoru Inoue, Matthew J. Smola, David M. Lee, Megan D. Schertzer, Joshua S. Wooten, Allison R. Baker, Daniel Sprague, David W. Collins, Christopher R. Horning, Shuo Wang (+4 others)
2018 Nature Genetics  
In contrast to proteins, lncRNAs with similar functions often lack linear sequence homology; thus, the identification of function in one lncRNA rarely informs the identification of function in others.  ...  We developed a sequence comparison method to deconstruct linear sequence relationships in lncRNAs and Results Kmer-based quantitation as a means to compare lncRNA sequence content We hypothesized that  ...  This work was supported by National Institutes of Health (NIH) Grants GM121806 and GM105785, Basil O'Connor Award  ... 
doi:10.1038/s41588-018-0207-8 pmid:30224646 pmcid:PMC6262761 fatcat:xyknj3hynbcbnap6ufzlb5lqn4

Genome-Wide Identification of TCP Family Transcription Factors in Medicago truncatula Reveals Significant Roles of miR319-Targeted TCPs in Nodule Development

Hongfeng Wang, Hongwei Wang, Rong Liu, Yiteng Xu, Zhichao Lu, Chuanen Zhou
2018 Frontiers in Plant Science  
Taken together, this study systematically analyzes the MtTCP gene family at a genomewide level and their possible functions in nodulation, which lay the basis for further explorations of MtmiR319/MtTCPs  ...  TCP proteins, the plant-specific transcription factors, are involved in the regulation of multiple aspects of plant development among different species, such as leaf development, branching, and flower  ...  (A) Phylogenetic tree was generated based on the full-length protein sequences of all MtTCP genes.  ... 
doi:10.3389/fpls.2018.00774 pmid:29942322 pmcid:PMC6004737 fatcat:iusagah325b4povn37rvy4vmzq

The Late Embryogenesis Abundant Protein Family in Cassava (Manihot esculenta Crantz): Genome-Wide Characterization and Expression during Abiotic Stress

Chunlai Wu, Wei Hu, Yan Yan, Weiwei Tie, Zehong Ding, Jianchun Guo, Guangyuan He
2018 Molecules  
In this study, 26 LEA members were genome-wide identified from cassava, which were clustered into seven subfamily according to evolutionary relationship, protein motif, and gene structure analyses.  ...  Most of the LEA protein families have a unique subcellular localization, which is involved in protecting the stability of cells under stress conditions [3, 14] .  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules23051196 pmid:29772750 fatcat:oqkfaqpmlrg2bam7antp6dbp6e

Evolutionary Divergence and Biased Expression of NAC Transcription Factors in Hexaploid Bread Wheat (Triticum aestivum L.)

Jianhui Ma, Meng Yuan, Bo Sun, Daijing Zhang, Jie Zhang, Chunxi Li, Yun Shao, Wei Liu, Lina Jiang
2021 Plants  
The protein structure results showed that TaNAC was relatively conservative at the N-terminal that contains five subdomains.  ...  All these TaNACs were divided into Group I and Group II by phylogenetic analysis, and the TaNACs in Group I should undergo strong artificial selection based on single nucleotide polymorphism (SNP) analysis  ...  From the above results, we found three types of evolutionary relationship, including a one-to-one relationship, a cluster-to-cluster relationship, and a one-to-cluster relationship.  ... 
doi:10.3390/plants10020382 pmid:33671285 pmcid:PMC7922369 fatcat:h5xkkrh2tnh67auciohh3gjnna

Genome-wide Identification, Classification and Expression Analysis of the Mildew Resistance Locus O ( MLO ) Gene Family in Sweet Orange ( Citrus sinensis )

Li-Ping Liu, Jin-Wang Qu, Xiao-Qu Yi, Huan-Huan Huang
2017 Brazilian Archives of Biology and Technology  
These findings will facilitate further studies of evolutionary pattern and biological functions of MLO genes in sweet orange.  ...  Survey of their chromosomal distributions uncovered that 14 CisMLOs are localized across 6 chromosomes.  ...  ACKNOWLEDGMENTS This research was supported by the Doctoral Scientific Research and Development Fund of Yangtze University (801190010130 and 801190010131).  ... 
doi:10.1590/1678-4324-2017160474 fatcat:nkxrxiqr2rhzppd4duceehf4ni

Discovering functions and revealing mechanisms at molecular level from biological networks

Shihua Zhang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen
2007 Proteomics  
The contents of the survey cover global topological properties and local structural characteristics, network motifs, network comparison and query, detection of functional modules and network motifs, function  ...  individual component level but at a system-wide level.  ...  of these networks and revealing evolutionary mechanisms at a system-wide level.  ... 
doi:10.1002/pmic.200700095 pmid:17703505 fatcat:spdclsqf4rdjxkxa7sts4c5u6q

Genome-wide Identification and Expression Analyses of Homeodomain-leucine Zipper Family Genes Reveal Their Involvement in Stress Response in Apple (Malus × domestica)

Quanyan Zhang, Tao Chen, Xun Wang, Jiahui Wang, Kaidi Gu, Jianqiang Yu, Dagang Hu, Yujin Hao
2021 Horticultural Plant Journal  
Subcellular localization and three-dimensional structural analysis revealed that MdHDZ3 was a nuclear-localized protein.  ...  They were assembled into four subgroups according to the classification in Arabidopsis, where MdHDZs in the same subgroup had similar gene structures and conserved protein motifs.  ...  Phylogenetic tree, gene structure and conserved motif analysis of the MdHDZ genes in apple To explore the evolutionary relationship among the HD-Zip proteins in apple, pear, strawberry, peach and Arabidopsis  ... 
doi:10.1016/j.hpj.2021.04.003 fatcat:x64fc23mqnf6lfa7xwdsrvrvdu
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