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Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence

Adriano Barbosa-Silva, Venkata P Satagopam, Reinhard Schneider, J Miguel Ortega
2008 BMC Bioinformatics  
We have developed a method to cluster cognate proteins from multiple organisms beginning with only one sequence, through connectivity saturation with that Seed sequence.  ...  It is extremely important to comparative biology that related proteins be identified as members of the same cognate group, since a characterized putative homolog could be used to find clues about the function  ...  Acknowledgements We would like to sincerely thank Darren A.  ... 
doi:10.1186/1471-2105-9-141 pmid:18321373 pmcid:PMC2277401 fatcat:lutdw2pgcvevpf7nbd7plmpfry

Archaeosortases and Exosortases Are Widely Distributed Systems Linking Membrane Transit with Posttranslational Modification

D. H. Haft, S. H. Payne, J. D. Selengut
2011 Journal of Bacteriology  
Multiple new prokaryotic C-terminal protein-sorting signals were found that reprise the tripartite architecture shared by LPXTG and PEP-CTERM: motif, TM helix, basic cluster.  ...  A picture emerges of an ancient and now well-differentiated superfamily of deeply membrane-embedded protein-processing enzymes.  ...  Alignment of multiple C-terminal putative protein-sorting signals from a single species often shows apparent sequence homology that runs through the TM domain and is not limited to the signature motif  ... 
doi:10.1128/jb.06026-11 pmid:22037399 pmcid:PMC3256604 fatcat:pefplcacfjfkre4mk4dspvw5ju

mRNA/protein sequence complementarity and its determinants: The impact of affinity scales

Lukas Bartonek, Bojan Zagrovic, Nikolay V. Dokholyan
2017 PLoS Computational Biology  
It has recently been demonstrated that the nucleobase-density profiles of mRNA coding sequences are related in a complementary manner to the nucleobase-affinity profiles of their cognate protein sequences  ...  obtained from experimental structures of RNA-protein complexes.  ...  The sequences of mRNAs and their cognate proteins are, of course, linked by the universal genetic code.  ... 
doi:10.1371/journal.pcbi.1005648 pmid:28750009 pmcid:PMC5549747 fatcat:vvdrz5dds5aivpsqdv5zvq4kw4

Developing microRNA screening as a functional genomics tool for disease research

Derek Lemons, Mano R. Maurya, Shankar Subramaniam, Mark Mercola
2013 Frontiers in Physiology  
ACKNOWLEDGMENTS Mark Mercola acknowledges research support from the NIH (R33HL088266 and R01HL113601), Mathers Charitable Trust, California Institute for Regenerative Medicine (RC1-000132) and the Fondation  ...  Shankar Subramaniam acknowledges research support from the NIH (R33HL087375, U54GM69338, P01DK074868, R01HL106579, and R01HL108735). miRNA screening is supported by NIH P30AR061303 and P30CA030199.  ...  One approach FIGURE 2 | Computational and experimental strategies to identify miRNA targets. miRNAs target multiple proteins, and in certain instances a single family of miRNAs target multiple proteins  ... 
doi:10.3389/fphys.2013.00223 pmid:23986717 pmcid:PMC3753477 fatcat:vkfd2mejk5ejvem5heyoagx3ae

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

Dimitrios G Zisoulis, Michael T Lovci, Melissa L Wilbert, Kasey R Hutt, Tiffany Y Liang, Amy E Pasquinelli, Gene W Yeo
2010 Nature Structural & Molecular Biology  
A single miRNA can potentially repress hundreds of genes by binding with partial sequence complementarity to mRNAs 3,4 .  ...  The identification and analysis of sequences directly associated with Argonaute protein in vivo in C. elegans has enabled the discovery of distinct features related to this core component of the miRNA-induced  ...  To characterize the sequence properties of ALG-1 binding sites, we subjected CDCs and a control set of random derived clusters (RDCs) to a battery of computational analyses.  ... 
doi:10.1038/nsmb.1745 pmid:20062054 pmcid:PMC2834287 fatcat:hohuu3ski5dtbea4ink5i54eha

Reshaping of the Arabidopsis thaliana proteome landscape and co-regulation of proteins in development and immunity [article]

Mona Bassal, Petra Majovsky, Domenika Thieme, Tobias Herr, Mohammad Abukhalaf, Mohamed Ayash, MHD Rami Al Shweiki, Carsten Proksch, Ali Hmedat, Jörg Ziegler, Steffan Neumann, Wolfgang Hoehenwarter
2020 bioRxiv   pre-print
Among others, the data suggest a potential function of RD26 and other NAC transcription factors in seed development related to desiccation tolerance as well as a possible function of Cysteine-rich Receptor-like  ...  The extensive coverage of the Arabidopsis proteome in various biological scenarios presents a rich resource to plant biologists that we make available to the community.  ...  The proteins in cluster 7 are very specific to the seed proteome.  ... 
doi:10.1101/2020.03.09.978627 fatcat:n6beqrdamrb4hb4wqh6f3bfnvi

Transcriptional profiling reveals distinct classes of parathyroid tumors in PHPT

James Koh, Joyce A Hogue, Sanziana A Roman, Randall P Scheri, Hèléne Fradin, David L Corcoran, Julie A Sosa
2018 Endocrine-Related Cancer  
RNAseq and proteomic analysis identified a candidate set of differentially expressed genes highly correlated with calcium-sensing capacity.  ...  Subsequent quantitative assessment of the expression levels of these genes in an independent cohort of parathyroid tumors confirmed that calcium-sensitive tumors cluster in a discrete transcriptional profile  ...  Tumors derived from PHPT patients with osteoporosis fell almost exclusively within Clusters 2 and 3, with only a single instance found in Cluster 1.  ... 
doi:10.1530/erc-17-0470 pmid:29475894 fatcat:ruorcgapmzajzejc5qc25q52ne

Origins and Diversification of a Complex Signal Transduction System in Prokaryotes

K. Wuichet, I. B. Zhulin
2010 Science Signaling  
While tracing its evolutionary history, we also developed a classification scheme that revealed more than a dozen distinct classes of chemotaxis systems, enabling future predictive modeling of chemotactic  ...  Article Tools;3/128/ra50 Visit the online version of this article to access the personalization and article tools: Materials Supplemental  ...  domains of cognate response regulators primarily targeting multiple DNA promoters) to the system that links multiple inputs (sensory domains of MCPs) to a single output (CheY to the flagellar motor).  ... 
doi:10.1126/scisignal.2000724 pmid:20587806 pmcid:PMC3401578 fatcat:yqpg5mnj25aotbe6hxzwwkcuta

Evolution of Function of a Fused Metazoan tRNA Synthetase

P. S. Ray, J. C. Sullivan, J. Jia, J. Francis, J. R. Finnerty, P. L. Fox
2010 Molecular biology and evolution  
The ERS and PRS catalytic domains in multiple bilaterian taxa are linked by variable number of helix-turn-helix domains referred to as WHEP-TRS domains.  ...  The glutamyl-prolyl tRNA synthetase (EPRS) of bilaterian animals is unique among AARSs, containing two functional enzymes catalyzing ligation of glutamate and proline to their cognate transfer RNAs (tRNAs  ...  Acknowledgment This work was supported by the National Institute of Health grants P01 HL029582, P01 HL076491, and R01 GM086430 (to P.L.F.).  ... 
doi:10.1093/molbev/msq246 pmid:20829344 pmcid:PMC3002251 fatcat:fj6hwv4omnhthbukompqcypqaa

Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level

Dalila Bensaddek, Vikram Narayan, Armel Nicolas, Alejandro Brenes Murillo, Anton Gartner, Cynthia J. Kenyon, Angus I. Lamond
2016 Proteomics  
The ten control animals clustered tightly together, distinct from the ten heat-shocked individ-uals.  ...  Results Optimization of protein extraction and data acquisition from single nematodes We optimized a lysis workflow that allows proteome extraction from single nematodes, reducing losses using a single  ... 
doi:10.1002/pmic.201500264 pmid:26552604 pmcid:PMC4819713 fatcat:4q7lcjdulfgu5esk2xhmbhggri

From Fuzziness to Precision Medicine: On the Rapidly Evolving Proteomics with Implications in Mitochondrial Connectivity to Rare Human Disease

Khaled A. Aly, Mohamed Taha Moutaoufik, Sadhna Phanse, Qingzhou Zhang, Mohan Babu
2021 iScience  
In this perspective article, we identified 21 mt proteins from public repositories that associate with RCC deficiency, MELAS, or ARSACS, engaging in a relatively small number of protein-protein interactions  ...  (PPIs), underscoring the need for advanced proteomic and interactomic platforms to uncover the complete scope of mt connectivity to RDs.  ...  Rapid developments in sorting techniques and single-cell RNA sequencing have made it possible to capture cell types of interest on a single cell level.  ... 
doi:10.1016/j.isci.2020.102030 pmid:33521598 pmcid:PMC7820543 fatcat:awxqyvbttrdyvnihnqxvn2qlme

Intraspecies Competition in Serratia marcescens Is Mediated by Type VI-Secreted Rhs Effectors and a Conserved Effector-Associated Accessory Protein

Juliana Alcoforado Diniz, Sarah J. Coulthurst, P. J. Christie
2015 Journal of Bacteriology  
Multiple antibacterial effectors can be delivered by these systems, with diverse activities against target cells and distinct modes of secretion.  ...  One of these was shown to act as a DNase toxin, while the other contains a novel, cytoplasmic-acting toxin domain.  ...  ACKNOWLEDGMENTS We thank Maximilian Fritsch for construction of strain MJF15, N. Gotoh for strain SM39, and Bill Hunter and all the members of the S.J.C. group for advice and discussion.  ... 
doi:10.1128/jb.00199-15 pmid:25939831 pmcid:PMC4524185 fatcat:k3qsa3d66jhnnnu35b2gj3m3ma

Combined Proteomics/Genomics Approach Reveals Proteomic Changes of Mature Virions as a Novel Poxvirus Adaptation Mechanism

Marica Grossegesse, Joerg Doellinger, Alona Tyshaieva, Lars Schaade, Andreas Nitsche
2017 Viruses  
While the overall viral genome sequence was stable during passaging, proteomics revealed multiple changes in the virion composition.  ...  To elucidate adaptation mechanisms of poxviruses, we isolated cowpox virus particles from a rat and passaged them five times in a human and a rat cell line.  ...  The authors are grateful to Andreas Kurth for providing crust material from infected rats. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/v9110337 pmid:29125539 pmcid:PMC5707544 fatcat:icaaryymh5dfblxcwmxrtersdq

Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release

Brian J Haas, Jennifer R Wortman, Catherine M Ronning, Linda I Hannick, Roger K Smith, Rama Maiti, Agnes P Chan, Chunhui Yu, Maryam Farzad, Dongying Wu, Owen White, Christopher D Town
2005 BMC Biology  
Since the initial publication of its complete genome sequence, Arabidopsis thaliana has become more important than ever as a model for plant research.  ...  However, the initial genome annotation was submitted by multiple centers using inconsistent methods, making the data difficult to use for many applications.  ...  Finally, we are indebted to NSF for their long and continuous support of this project (Cooperative Agreement. DBI 9813586).  ... 
doi:10.1186/1741-7007-3-7 pmid:15784138 pmcid:PMC1082884 fatcat:jw5tyx6eubea7fb5yczxnc4ynq

Global Analysis of Protein Palmitoylation in African Trypanosomes

Brian T. Emmer, Ernesto S. Nakayasu, Christina Souther, Hyungwon Choi, Tiago J. P. Sobreira, Conrad L. Epting, Alexey I. Nesvizhskii, Igor C. Almeida, David M. Engman
2010 Eukaryotic Cell  
A total of 124 palmitoylated proteins were identified, with an estimated false discovery rate of 1.0%.  ...  This palmitoyl proteome includes all of the known palmitoyl proteins in procyclic-stage T. brucei as well as several proteins whose homologues are palmitoylated in other organisms.  ...  5G12RR008124-16A1) for use of the LC-MS instrument.  ... 
doi:10.1128/ec.00248-10 pmid:21193548 pmcid:PMC3067466 fatcat:cib2fd3wcfa4zblb27rtabmnrq
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