Integrating multiple 'omics' analysis for microbial biology: application and methodologies

W Zhang, F Li, L Nie - Microbiology, 2010 - microbiologyresearch.org
Recent advances in various 'omics' technologies enable quantitative monitoring of the
abundance of various biological molecules in a high-throughput manner, and thus allow …

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 …

A ternary AppA–PpsR–DNA complex mediates light regulation of photosynthesis-related gene expression

A Winkler, U Heintz, R Lindner, J Reinstein… - Nature structural & …, 2013 - nature.com
The anoxygenic phototrophic bacterium Rhodobacter sphaeroides uses different energy
sources, depending on environmental conditions including aerobic respiration or, in the …

Reconstruction of the core and extended regulons of global transcription factors

YS Dufour, PJ Kiley, TJ Donohue - PLOS genetics, 2010 - journals.plos.org
The processes underlying the evolution of regulatory networks are unclear. To address this
question, we used a comparative genomics approach that takes advantage of the large …

Global analysis of photosynthesis transcriptional regulatory networks

S Imam, DR Noguera, TJ Donohue - PLoS genetics, 2014 - journals.plos.org
Photosynthesis is a crucial biological process that depends on the interplay of many
components. This work analyzed the gene targets for 4 transcription factors: FnrL, PrrA, CrpK …

Antisense RNA asPcrL regulates expression of photosynthesis genes in Rhodobacter sphaeroides by promoting RNase III-dependent turn-over of puf mRNA

CM Reuscher, G Klug - RNA biology, 2021 - Taylor & Francis
Anoxygenic photosynthesis is an important pathway for Rhodobacter sphaeroides to
produce ATP under oxygen-limiting conditions. The expression of its photosynthesis genes …

An integrated approach to reconstructing genome-scale transcriptional regulatory networks

S Imam, DR Noguera, TJ Donohue - PLoS Computational Biology, 2015 - journals.plos.org
Transcriptional regulatory networks (TRNs) program cells to dynamically alter their gene
expression in response to changing internal or environmental conditions. In this study, we …

Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides

L Peña-Castillo, RG Mercer, A Gurinovich, SJ Callister… - BMC genomics, 2014 - Springer
Abstract Background The genus Rhodobacter contains purple nonsulfur bacteria found
mostly in freshwater environments. Representative strains of two Rhodobacter species, R …

Pseudomonas syringae Two-Component Response Regulator RhpR Regulates Promoters Carrying an Inverted Repeat Element

X Deng, L Lan, Y Xiao, M Kennelly… - Molecular plant …, 2010 - Am Phytopath Society
The two-component system RhpRS was identified in Pseudomonas syringae as a regulator
of the genes encoding the type III secretion system and type III effector proteins (together …

The Vitamin B12-Dependent Photoreceptor AerR Relieves Photosystem Gene Repression by Extending the Interaction of CrtJ with Photosystem Promoters

M Fang, CE Bauer - MBio, 2017 - Am Soc Microbiol
Purple nonsulfur bacteria adapt their physiology to a wide variety of environmental
conditions often through the control of transcription. One of the main transcription factors …