Endocytosis and signaling: cell logistics shape the eukaryotic cell plan

S Sigismund, S Confalonieri, A Ciliberto… - Physiological …, 2012 - journals.physiology.org
Our understanding of endocytosis has evolved remarkably in little more than a decade. This
is the result not only of advances in our knowledge of its molecular and biological workings …

The origin and early evolution of eukaryotes in the light of phylogenomics

EV Koonin - Genome biology, 2010 - Springer
The origin and early evolution of eukaryotes in the light of phylogenomics | Genome Biology
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Insights into SAGA function during gene expression

S Rodríguez‐Navarro - EMBO reports, 2009 - embopress.org
Histone modifications are a crucial source of epigenetic control. SAGA (Spt–Ada–Gcn5
acetyltransferase) is a chromatin‐modifying complex that contains two distinct enzymatic …

E3 ligase Rad18 promotes monoubiquitination rather than ubiquitin chain formation by E2 enzyme Rad6

RG Hibbert, A Huang, R Boelens… - Proceedings of the …, 2011 - National Acad Sciences
In ubiquitin conjugation, different combinations of E2 and E3 enzymes catalyse either
monoubiquitination or ubiquitin chain formation. The E2/E3 complex Rad6/Rad18 …

Towards genome-scale signalling-network reconstructions

DR Hyduke, BØ Palsson - Nature Reviews Genetics, 2010 - nature.com
Biological signalling networks allow living organisms to issue an integrated response to
current conditions and make limited predictions about future environmental changes. Small …

RNA damage in biological conflicts and the diversity of responding RNA repair systems

AM Burroughs, L Aravind - Nucleic acids research, 2016 - academic.oup.com
RNA is targeted in biological conflicts by enzymatic toxins or effectors. A vast diversity of
systems which repair or 'heal'this damage has only recently become apparent. Here, we …

Structural basis of generic versus specific E2–RING E3 interactions in protein ubiquitination

M Gundogdu, H Walden - Protein Science, 2019 - Wiley Online Library
Protein ubiquitination is a fundamental regulatory component in eukaryotic cell biology,
where a cascade of ubiquitin activating (E1), conjugating (E2), and ligating (E3) enzymes …

New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing

AM Burroughs, Y Ando, L Aravind - Wiley Interdisciplinary …, 2014 - Wiley Online Library
Our understanding of the pervasive involvement of small RNAs in regulating diverse
biological processes has been greatly augmented by recent application of deep …

Polyubiquitin Chains Linked by Lysine Residue 48 (K48) Selectively Target Oxidized Proteins In Vivo

S Manohar, S Jacob, J Wang, KA Wiechecki… - Antioxidants & redox …, 2019 - liebertpub.com
Aims: Ubiquitin is a highly conserved protein modifier that heavily accumulates during the
oxidative stress response. Here, we investigated the role of the ubiquitination system …

Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package

F Almeida‐Silva, Y Van de Peer - Methods in Ecology and …, 2023 - Wiley Online Library
Comparative genomics has become an indispensable part of modern biology due to the
advancements in high‐throughput sequencing technologies and the accumulation of …