Biology subjects

Iyer, L. M.

Publications and source records attributed to Iyer, L. M..

3 recordsLinked to original sources

bioRxiv2017

A tangled tale of convergence and divergence: archaeal chromosomal proteins and Chromo-like domains in bacteria and eukaryotes

The Chromo-like superfamily of SH3-fold {beta}-barrel domains recognize epigenetic marks in eukaryotic proteins. Their provenance has been placed either in archaea, based on apparent structural similarity to chromatin-compacting Sul7d and Cren7 proteins, or in bacteria based on the presence of sequence homologs. Using sequence and structural evidence we establish that the archaeal Cren7/Sul7 proteins emerged from a zinc ribbon (ZnR) ancestor. Further, we show that the ancestral eukaryotic Chromo-like domains evolved from bacterial precursors acquired from early endosymbioses, which already possessed an aromatic cage for recognition of modified amino-groups. These bacterial versions are part of a radiation of secreted SH3-fold domains, which spawned both chromo-like domains and classical SH3 domains in the context of peptide-recognition in the peptidoglycan. This establishes that Cren7/Sul7 converged to a \"SH3\"-like state from a ZnR precursor via the loss of metal-chelation and acquisition of stronger hydrophobic interactions; it is unlikely to have participated in the evolution of the chromo-like domains. We show that archaea possess several Cren7/Sul7-related proteins with intact Zn-chelating ligands, which we predict to play previously unstudied roles in cell-division comparable to the PRC barrel.

bioinformatics↗

bioRxiv2017

The roles of Conserved Domains in DEMETER-Mediated Active DNA Demethylation in planta

DNA methylation plays critical roles in maintaining genome stability, genomic imprinting, transposon silencing, and development. In Arabidopsis genomic imprinting is established in the central cell by DEMETER (DME)-mediated active DNA demethylation, and is essential for seed viability. DME is a large polypeptide with multiple poorly characterized conserved domains. Here we show that the C-terminal enzymatic core of DME is sufficient to complement dme associated developmental defects. When targeted by a native DME promoter, nuclear-localized DME C-terminal region rescues dme seed abortion and pollen germination defects, and ameliorates CG hypermethylation phenotype in dme-2 endosperm. Furthermore, targeted expression of the DME N-terminal region in wild-type central cell induces dme-like seed abortion phenotype. Our results support a bipartite organization for DME protein, and suggest that the N-terminal region might have regulatory function such as assisting in DNA binding and enhancing the processivity of active DNA demethylation in heterochromatin targets.

plant biology↗

bioRxiv2016

Quod erat demonstrandum? No restriction endonuclease fold in MIF

It was claimed in a recently published article that MIF functions as an exo/endo-DNase mediating cell-death upon being induced by DNA damage and PARP1. MIF, for which tautomerase activity has been previously reported, is a member of the tautomerase superfamily which does not feature nucleases. The central premise of the authors to suggest that MIF functions as a DNase is the supposed structural relationship to nucleases of the Restriction endonuclease (REase) fold, which frequently but not always contain a motif of the form PD-(D/E)XK. However, we present evidence to show that this claim is entirely unsupported.

biochemistry↗