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Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins

S. Pasek, J.-L. Risler, P. Brezellec
2006 Bioinformatics  
We conclude that gene fusion/fission is a major contributor to the evolution of multi-domain bacterial proteins.  ...  We provide evidence showing that the contribution of gene fusion/fission to the evolution of multi-domain bacterial proteins is lower-bounded by 27% and upper-bounded by 64%.  ...  ACKNOWLEDGEMENTS The authors are grateful to Jean-Luc Ferat, Meriem El Karoui and to the members of ABI (University of Paris VI) for helpful discussions.  ... 
doi:10.1093/bioinformatics/btl135 pmid:16601004 fatcat:gqgrh7v2yzbo3iiuj4xzwglydm

The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome

Michael W. Gray, Gertraud Burger, Romain Derelle, Vladimír Klimeš, Michelle M. Leger, Matt Sarrasin, Čestmír Vlček, Andrew J. Roger, Marek Eliáš, B. Franz Lang
2020 BMC Biology  
In this regard, a key group is the jakobids, a clade of protists belonging to the eukaryotic supergroup Discoba, distinguished by having the most gene-rich and most bacteria-like mitochondrial genomes  ...  of this protist, identifying 864 candidate mitochondrial proteins.  ...  is mediated by a mtDNA-encoded, bacterial-type, multi-subunit RNAP.  ... 
doi:10.1186/s12915-020-0741-6 pmid:32122349 pmcid:PMC7050145 fatcat:g55whedl2bdibow3nt2tbbyu6i

The evolution of bacterial mechanosensitive channels

Ian R. Booth, Samantha Miller, Axel Müller, Laura Lehtovirta-Morley
2015 Cell Calcium  
The MscS family of proteins displays considerable plasticity in their current forms and the variants may have arisen by a variety of routes, including duplication, fusion, fission and evolved expression  ...  The exception is ybdG in Klebsiella, which appears to have been transposed and now lies between lacI and a gene for a major facilitator membrane protein.  ... 
doi:10.1016/j.ceca.2014.12.011 pmid:25591932 fatcat:6ll2r6i3ofc75blwxeaatd3myu

Division of labour in a matrix, rather than phagocytosis or endosymbiosis, as a route for the origin of eukaryotic cells

Andrew Bateman
2020 Biology Direct  
The model is compatible with the loss of archaeal lipid biochemistry while retaining archaeal genes and provides a route for the development of membranous organelles such as the Golgi apparatus and endoplasmic  ...  A version is presented in which an extracellular space (the third-space), serves as a proxy cytoplasm for mixed populations of archaea and bacteria to "merge" as a transitionary complex without obligatory  ...  , allows increased cell fusion (a relic of which is the fusion/fission cycle of extant mitochondria) and this further amplifies the exchange of genetic material until structures (called here multi-genomes  ... 
doi:10.1186/s13062-020-00260-9 pmid:32345370 fatcat:623ydkd7affufiuzo6l2kqbtye

Phylogenetic Profiling of Mitochondrial Proteins and Integration Analysis of Bacterial Transcription Units Suggest Evolution of F1Fo ATP Synthase from Multiple Modules

Yulong Niu, Shayan Moghimyfiroozabad, Sepehr Safaie, Yi Yang, Elizabeth A. Jonas, Kambiz N. Alavian
2017 Journal of Molecular Evolution  
contributor to evolution of multi-domain bacterial proteins.  ...  Biochim Biophys Acta 1757(9–10):1400–1405 Pasek S, Risler JL, Brezellec P (2006) Gene fusion/fission is a major Huynen M, Snel B, Lathe W 3rd, Bork P (2000) Predicting protein  ... 
doi:10.1007/s00239-017-9819-3 pmid:29177973 pmcid:PMC5709465 fatcat:v6dyqv5unbfnfermrcbgxrvvp4

Bioinformatics in microbial biotechnology--a mini review

Arvind K Bansal
2005 Microbial Cell Factories  
to administer vaccines, the development of protein biomarkers for various bacterial diseases, and better understanding of host-bacteria interaction to prevent bacterial infections.  ...  Despite the fast paced global effort, the current analysis is limited by the lack of available gene-functionality from the wet-lab data, the lack of computer algorithms to explore vast amount of data with  ...  Acknowledgements Due to the limited scope of this review, the author was restricted to acknowledge a small number of relevant publications contributing directly to microbial bioinformatics.  ... 
doi:10.1186/1475-2859-4-19 pmid:15985162 pmcid:PMC1182391 fatcat:yhfb3z3e2zhoxd6yucafktp2gu

The ParA's function is realized by two separate proteins in the partitioning system of Myxococcus plasmid pMF1 [article]

Duo-hong sheng, Xiao-jing Chen, Ya-jie Li, Jing-jing Wang, Li Zhuo, Yue-zhong Li
2020 bioRxiv   pre-print
The par operon in the sole myxobacterial plasmid pMF1 includes a function-unknown parC gene in front of the classical parA and parB genes.  ...  The present results highlight that ParC functions as a part of ParA to support its soluble expression and function, and the separation of ParC and ParA into two proteins in structure enables the ParC '  ...  Gene fusion/fission is a major contributor to 511 evolution of multi-domain bacterial proteins. Bioinformatics. 2006;22(12):1418-512 1423.  ... 
doi:10.1101/2020.07.24.219303 fatcat:x42h45kaujhktmrkztc7tgjbwm

ParC, a New Partitioning Protein, Is Necessary for the Active Form of ParA From Myxococcus pMF1 Plasmid

Duohong Sheng, Xiaojing Chen, Yajie Li, Jingjing Wang, Li Zhuo, Yuezhong Li
2021 Frontiers in Microbiology  
The results highlight that proximal location of parC before parA is critical to realize the functions of ParA in the partition of Myxococcus plasmid pMF1 and shed light on a new mechanism to realize a  ...  The pMF1 plasmid from Myxococcus fulvus 124B02 has a par operon encoding a small acidic protein, ParC, in addition to type I ParA and ParB homologs.  ...  Gene fusion/fission is a major contributor to the evolution of multi-domain proteins (Pasek et al., 2006) .  ... 
doi:10.3389/fmicb.2020.623699 pmid:33519784 pmcid:PMC7843461 fatcat:g4ajgoqudfdkzonuef5idektb4

Synthaser: a CD-Search enabled Python toolkit for analysing domain architecture of fungal secondary metabolite megasynth(et)ases

Cameron L. M. Gilchrist, Yit-Heng Chooi
2021 Fungal Biology and Biotechnology  
Conclusions Synthaser is an easy to use tool that represents a significant upgrade to previous domain architecture analysis tools.  ...  The backbones of a large proportion of fungal SMs are generated through the action of large, multi-domain megasynth(et)ases such as polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs  ...  fusion, fission, duplication and exon shuffling [3] [4] [5] .  ... 
doi:10.1186/s40694-021-00120-9 pmid:34763725 pmcid:PMC8582187 fatcat:tsln7hrhnbguzjj2mxmibsj3fm

Identification of polycistronic transcriptional units and non-canonical introns in green algal chloroplasts based on long-read RNA sequencing data

Xiaoxiao Zou, Heroen Verbruggen, Tianjingwei Li, Jun Zhu, Zou Chen, Henqi He, Shixiang Bao, Jinhua Sun
2021 BMC Genomics  
In addition to clusters of genes from the same pathway, we identified a series of PTUs of up to nine genes whose function in the plastid is not understood.  ...  Our data also revealed a type of non-canonical Group II introns, with a deviant secondary structure and intronic ORFs lacking known splicing or mobility domains.  ...  Acknowledgements We are very grateful to Peng Li, Fengshou Wang  ... 
doi:10.1186/s12864-021-07598-y pmid:33892645 fatcat:6r22hy3m7ffppm7qy2wfaaclkq

Role of phospholipid signalling in plant environmental responses

E. Ruelland, V. Kravets, M. Derevyanchuk, J. Martinec, A. Zachowski, I. Pokotylo
2015 Environmental and Experimental Botany  
The conversion of lipids is catalysed by the hydrolytic activity of phospholipases and by the action of lipid-kinases and lipid-phosphatases.  ...  Together they shape cell metabolism via binding to downstream protein targets, thus affecting enzymatic activities, vesicle trafficking and ion fluxes.  ...  We would like to thank Prof. Jill Farrant (Department of Molecular and Cell Biology, University of Cape Town, South Africa) for carefully reading the manuscript.  ... 
doi:10.1016/j.envexpbot.2014.08.009 fatcat:6szixt3fu5egzaitwr3etiqelq

Dealing with Stress: Defective Metabolic Adaptation in Chronic Obstructive Pulmonary Disease Pathogenesis

Charalambos Michaeloudes, Pankaj K. Bhavsar, Sharon Mumby, Kian Fan Chung, Ian M. Adcock
2017 Annals of the American Thoracic Society  
During evolution, a considerable 67 proportion of the bacterial genome was transferred to the eukaryotic nucleus.  ...  Thus, the majority of 68 mitochondrial proteins are encoded by the nuclear genome (10).  ...  into linear or branched networks as a result of continuous cycles of fission and fusion, mediated by 157 multi-domain dynamin-related GTPases (30).  ... 
doi:10.1513/annalsats.201702-153aw pmid:29161091 pmcid:PMC5711272 fatcat:qwsrivozkrgctbeld6bditjswq

The rise of mitochondria in medicine

Martin Picard, Douglas C. Wallace, Yan Burelle
2016 Mitochondrion (Amsterdam. Print)  
Increasing knowledge of the bioenergetic aspects of human disease has provided new opportunities for diagnosis, therapy, prevention, and in connecting various domains of medicine.  ...  In this article, we overview specific aspects of mitochondrial biology that have contributed to -and likely will continue to enhance the progress of modern medicine.  ...  ., sedentary behavior) is a major risk factor for AD.  ... 
doi:10.1016/j.mito.2016.07.003 pmid:27423788 pmcid:PMC5023480 fatcat:eusmoxj6xzepfmhoyjjgpdupju

Abstracts of the 48th Annual CSBMCB Meeting / Résumés de la 48e assemblée annuelle de la SCBBMC

2005 Biochemistry and Cell Biology  
Fritzler 767 The role of protein synthesis in the regulation of mRNA partitioning to the endoplasmic reticulum R.S. Lerner, M.C. Reedy, and C.V.  ...  766 Characterization of a novel cytoplasmic organelle, GW bodies, as a site of mRNA localization in normal and malignant breast cell lines and tissues L.M. Luft, E.K.L. Chan, M.J.  ...  We identified Hrr25p, a casein kinase that distributes to numerous cellular structures including spindle pole bodies, as a major contributor to Nup53p phosphorylation.  ... 
doi:10.1139/o05-907 fatcat:ioe6ipip45hzxnhmxus4egg7te

2017 ASCB Annual Meeting Abstracts

David G. Drubin
2017 Molecular Biology of the Cell  
Another discovery was the identification of a new lysosomal sorting pathway for GPCRs that requires ALG-interacting protein (ALIX) and arrestin-related domain containing protein-3 (ARRDC3).  ...  The ubiquitin ligase Rsp5, the yeast homolog of human Nedd4, is a key mediator of protein quality control at the PM.  ...  dynamic pool of actin and its mode of coupling to inner-leaflet lipids is lacking.  ... 
doi:10.1091/mbc.e17-10-0618 pmid:29237772 pmcid:PMC5739290 fatcat:3msjrn3omzcybfanlagykayauy
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