Lakshminarayan M. Iyer
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View article: Biliverdin reductase A is a major determinant of protective NRF2 signaling
Biliverdin reductase A is a major determinant of protective NRF2 signaling Open
Biliverdin reductase A (BVRA), the terminal enzyme in heme catabolism, generates the neuroprotective and lipophilic antioxidant bilirubin. Here, we identify a nonenzymatic role for BVRA in redox regulation. Through phylogenetic, genetic, b…
View article: Identification of a depupylation regulator for an essential enzyme in <i>Mycobacterium tuberculosis</i>
Identification of a depupylation regulator for an essential enzyme in <i>Mycobacterium tuberculosis</i> Open
In Mycobacterium tuberculosis (Mtb) , proteins that are posttranslationally modified with a prokaryotic ubiquitin-like protein (Pup) can be degraded by bacterial proteasomes. A single Pup-ligase and depupylase shape the pupylome, but the m…
View article: A sequence-specific RNA acetylation catalyst
A sequence-specific RNA acetylation catalyst Open
N4-acetylcytidine (ac4C) is a ubiquitous RNA modification incorporated by cytidine acetyltransferase enzymes. Here, we report the biochemical characterization of Thermococcus kodakarensis Nat10 (TkNat10), an RNA acetyltransferase involved …
View article: The Prokaryotic Roots of Eukaryotic Immune Systems
The Prokaryotic Roots of Eukaryotic Immune Systems Open
Over the past two decades, studies have revealed profound evolutionary connections between prokaryotic and eukaryotic immune systems, challenging the notion of their unrelatedness. Immune systems across the tree of life share an operationa…
View article: Identification of a proteolysis regulator for an essential enzyme in<i>Mycobacterium tuberculosis</i>
Identification of a proteolysis regulator for an essential enzyme in<i>Mycobacterium tuberculosis</i> Open
In Mycobacterium tuberculosis proteins that are post-translationally modified with Pup, a prokaryotic ubiquitin-like protein, can be degraded by proteasomes. While pupylation is reversible, mechanisms regulating substrate specificity have …
View article: Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems
Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems Open
While nucleic acid-targeting effectors are known to be central to biological conflicts and anti-selfish element immunity, recent findings have revealed immune effectors that target their building blocks and the cellular energy currency—fre…
View article: VirB, a key transcriptional regulator of <i>Shigella</i> virulence, requires a CTP ligand for its regulatory activities
VirB, a key transcriptional regulator of <i>Shigella</i> virulence, requires a CTP ligand for its regulatory activities Open
The VirB protein, encoded by the large virulence plasmid of Shigella spp., is a key transcriptional regulator of virulence genes. Without virB , Shigella cells are avirulent. On the virulence plasmid, VirB functions to offset transcription…
View article: VirB, a key transcriptional regulator of<i>Shigella</i>virulence, requires a CTP ligand for its regulatory activities
VirB, a key transcriptional regulator of<i>Shigella</i>virulence, requires a CTP ligand for its regulatory activities Open
The VirB protein, encoded by the large virulence plasmid of Shigella spp., is a key transcriptional regulator of virulence genes. Without a functional virB gene, Shigella cells are avirulent. On the virulence plasmid, VirB functions to off…
View article: Apprehending the NAD+–ADPr-Dependent Systems in the Virus World
Apprehending the NAD+–ADPr-Dependent Systems in the Virus World Open
NAD+ and ADP-ribose (ADPr)-containing molecules are at the interface of virus–host conflicts across life encompassing RNA processing, restriction, lysogeny/dormancy and functional hijacking. We objectively defined the central components of…
View article: Discovering Biological Conflict Systems Through Genome Analysis: Evolutionary Principles and Biochemical Novelty
Discovering Biological Conflict Systems Through Genome Analysis: Evolutionary Principles and Biochemical Novelty Open
Biological replicators, from genes within a genome to whole organisms, are locked in conflicts. Comparative genomics has revealed a staggering diversity of molecular armaments and mechanisms regulating their deployment, collectively termed…
View article: Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans
Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans Open
Several homologous domains are shared by eukaryotic immunity and programmed cell-death systems and poorly understood bacterial proteins. Recent studies show these to be components of a network of highly regulated systems connecting apoptot…
View article: Author response: Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans
Author response: Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans Open
Article Figures and data Abstract Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Several homologous domains are shared by e…
View article: GREB1: An evolutionarily conserved protein with a glycosyltransferase domain links ERα glycosylation and stability to cancer
GREB1: An evolutionarily conserved protein with a glycosyltransferase domain links ERα glycosylation and stability to cancer Open
GREB1 is an inducible cytoplasmic glycosyltransferase.
View article: Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts
Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts Open
Jumbo phages have attracted much attention by virtue of their extraordinary genome size and unusual aspects of biology. By performing a comparative genomics analysis of 224 jumbo phages, we suggest an objective inclusion criterion based on…
View article: Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea
Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea Open
A prominent epigenetic mechanism for gene regulation is methylation of cytosine bases in DNA. TET enzymes facilitate DNA demethylation by converting 5-methylcytosine (5mC) to oxidized methylcytosines (oxi-mCs). We show that oxi-mCs are gen…
View article: Mycobacterium tuberculosis Rv0991c Is a Redox-Regulated Molecular Chaperone
Mycobacterium tuberculosis Rv0991c Is a Redox-Regulated Molecular Chaperone Open
M. tuberculosis infections are responsible for more than 1 million deaths per year. Developing effective strategies to combat this disease requires a greater understanding of M. tuberculosis biology. As in all cells, protein quality contro…
View article: Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems
Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems Open
ABC ATPases form one of the largest clades of P-loop NTPase fold enzymes that catalyze ATP-hydrolysis and utilize its free energy for a staggering range of functions from transport to nucleoprotein dynamics. Using sensitive sequence and st…
View article: <i>Mycobacterium tuberculosis</i>Rv0991c is a redox-regulated molecular chaperone
<i>Mycobacterium tuberculosis</i>Rv0991c is a redox-regulated molecular chaperone Open
The bacterial pathogen Mycobacterium (M.) tuberculosis is the leading cause of death by an infectious disease among humans. Here, we describe a previously uncharacterized M. tuberculosis protein, Rv0991c, as a molecular chaperone that is a…
View article: Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity
Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity Open
Social cellular aggregation or multicellular organization pose increased risk of transmission of infections through the system upon infection of a single cell. The generality of the evolutionary responses to this outside of Metazoa remains…
View article: Corrigendum: The cyl Genes Reveal the Biosynthetic and Evolutionary Origins of the Group B Streptococcus Hemolytic Lipid, Granadaene
Corrigendum: The cyl Genes Reveal the Biosynthetic and Evolutionary Origins of the Group B Streptococcus Hemolytic Lipid, Granadaene Open
CORRECTION article Front. Microbiol., 25 February 2020 | https://doi.org/10.3389/fmicb.2020.00325
View article: Functional Innovation in the Evolution of the Calcium-Dependent System of the Eukaryotic Endoplasmic Reticulum
Functional Innovation in the Evolution of the Calcium-Dependent System of the Eukaryotic Endoplasmic Reticulum Open
The origin of eukaryotes was marked by the emergence of several novel subcellular systems. One such is the calcium (Ca2+)-stores system of the endoplasmic reticulum, which profoundly influences diverse aspects of cellular functi…
View article: Author response: Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity
Author response: Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity Open
Article Figures and data Abstract eLife digest Introduction Results and discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Social cellular aggregati…
View article: The cyl Genes Reveal the Biosynthetic and Evolutionary Origins of the Group B Streptococcus Hemolytic Lipid, Granadaene
The cyl Genes Reveal the Biosynthetic and Evolutionary Origins of the Group B Streptococcus Hemolytic Lipid, Granadaene Open
[This corrects the article DOI: 10.3389/fmicb.2019.03123.].
View article: The catalytic core of DEMETER guides active DNA demethylation in <i>Arabidopsis</i>
The catalytic core of DEMETER guides active DNA demethylation in <i>Arabidopsis</i> Open
The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the maternal genome in the central cell prior to fertilization and is essential for seed viability. DME preferentially targets small transposons that flank coding genes, influencin…
View article: Functional innovation in the evolution of the calcium-dependent system of the eukaryotic endoplasmic reticulum
Functional innovation in the evolution of the calcium-dependent system of the eukaryotic endoplasmic reticulum Open
The origin of eukaryotes was marked by the emergence of several novel subcellular systems. One such is the calcium (Ca 2+ )-stores system of the endoplasmic reticulum, which profoundly influences diverse aspects of cellular function includ…
View article: Unexpected Evolution of Lesion-Recognition Modules in Eukaryotic NER and Kinetoplast DNA Dynamics Proteins from Bacterial Mobile Elements
Unexpected Evolution of Lesion-Recognition Modules in Eukaryotic NER and Kinetoplast DNA Dynamics Proteins from Bacterial Mobile Elements Open
View article: The unexpected provenance of components in eukaryotic nucleotide-excision-repair and kinetoplast DNA-dynamics from bacterial mobile elements
The unexpected provenance of components in eukaryotic nucleotide-excision-repair and kinetoplast DNA-dynamics from bacterial mobile elements Open
Background Protein ‘weaponry’ deployed in biological conflicts between selfish elements and their hosts are increasingly recognized as being re-purposed for diverse molecular adaptations in the evolution of several uniquely eukaryotic syst…
View article: Games we play: Tetrahymena vs Chlamydomonas. Part 3 of series
Games we play: Tetrahymena vs Chlamydomonas. Part 3 of series Open
View article: Dressing up protozoans (Vital Staining): Tetrahymena Vorax Part 2
Dressing up protozoans (Vital Staining): Tetrahymena Vorax Part 2 Open
View article: Polymorphism, cannibalism, epigenetics, and biological conflict: The many stories of Tetrahymena vorax - Part I
Polymorphism, cannibalism, epigenetics, and biological conflict: The many stories of Tetrahymena vorax - Part I Open