Bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: redox control

E Bueno, S Mesa, EJ Bedmar… - Antioxidants & redox …, 2012 - liebertpub.com
Under a shortage of oxygen, bacterial growth can be faced mainly by two ATP-generating
mechanisms:(i) by synthesis of specific high-affinity terminal oxidases that allow bacteria to …

[HTML][HTML] Fe–S proteins that regulate gene expression

EL Mettert, PJ Kiley - Biochimica et Biophysica Acta (BBA)-Molecular Cell …, 2015 - Elsevier
Abstract Iron–sulfur (Fe–S) cluster containing proteins that regulate gene expression are
present in most organisms. The innate chemistry of their Fe–S cofactors makes these …

How life changes itself: The Read–Write (RW) genome

JA Shapiro - Physics of Life Reviews, 2013 - Elsevier
The genome has traditionally been treated as a Read-Only Memory (ROM) subject to
change by copying errors and accidents. In this review, I propose that we need to change …

Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria

OV Tsoy, DA Ravcheev, J Čuklina… - Frontiers in …, 2016 - frontiersin.org
Biological nitrogen fixation plays a crucial role in the nitrogen cycle. An ability to fix
atmospheric nitrogen, reducing it to ammonium, was described for multiple species of …

Iron-containing transcription factors and their roles as sensors

AS Fleischhacker, PJ Kiley - Current opinion in chemical biology, 2011 - Elsevier
Iron-binding transcription factors are widespread throughout the bacterial world and to date
are known to bind several types of cofactors, such as Fe2+, heme, or iron–sulfur clusters …

Multiple sensors provide spatiotemporal oxygen regulation of gene expression in a Rhizobium-legume symbiosis

PJ Rutten, H Steel, GA Hood, VK Ramachandran… - PLoS …, 2021 - journals.plos.org
Regulation by oxygen (O2) in rhizobia is essential for their symbioses with plants and
involves multiple O2 sensing proteins. Three sensors exist in the pea microsymbiont …

Tuning the modular Paracoccus denitrificans respirome to adapt from aerobic respiration to anaerobic denitrification

G Giannopoulos, MJ Sullivan, KR Hartop… - Environmental …, 2017 - Wiley Online Library
Bacterial denitrification is a respiratory process that is a major source and sink of the potent
greenhouse gas nitrous oxide. Many denitrifying bacteria can adjust to life in both oxic and …

Conservation of thiol‐oxidative stress responses regulated by SigR orthologues in actinomycetes

MS Kim, YS Dufour, JS Yoo, YB Cho… - Molecular …, 2012 - Wiley Online Library
Numerous thiol‐reactive compounds cause oxidative stress where cells counteract by
activation of survival strategies regulated by thiol‐based sensors. In Streptomyces …

Reassessing the Structure and Function Relationship of the O2 Sensing Transcription Factor FNR

EL Mettert, PJ Kiley - Antioxidants & Redox Signaling, 2018 - liebertpub.com
Abstract Significance: The Escherichia coli regulatory protein fumarate nitrate reduction
(FNR) mediates a global transcriptional response upon O2 deprivation. Spanning nearly 40 …

Graph splitting: a graph-based approach for superfamily-scale phylogenetic tree reconstruction

M Matsui, W Iwasaki - Systematic biology, 2020 - academic.oup.com
A protein superfamily contains distantly related proteins that have acquired diverse
biological functions through a long evolutionary history. Phylogenetic analysis of the early …