Comparative genomics sheds light on transcription factor-mediated regulation in the extreme acidophilic Acidithiobacillia representatives

Key Factors Governing Microbial Community in Extremely Acidic Mine Drainage (pH

(2022) Ye Huang et al.   Frontiers in Microbiology

Integrative Genomics Sheds Light on Evolutionary Forces Shaping the Acidithiobacillia Class Acidophilic Lifestyle

(2022) Carolina González-Rosales et al.   Frontiers in Microbiology

Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes

(2022) Luis Romero et al.   Frontiers in Microbiology

The transcriptional regulators of virulence for Pseudomonas aeruginosa: Therapeutic opportunity and preventive potential of its clinical infections

(2022) Xiaolong Shao et al.   Genes and Diseases

Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions

(2021) Ana Moya-Beltrán et al.   ISME Journal

Molecular Insights into the Copper-Sensitive Operon Repressor in Acidithiobacillus caldus

(2021) Shaoxiang Hou et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bioleaching for environmental remediation of toxic metals and metalloids: A review on soils, sediments, and mine tailings

(2021) Trung Hau Nguyen et al.   CHEMOSPHERE

Evaluation of the Abundance of DNA-Binding Transcription Factors in Prokaryotes

(2020) Israel Sanchez et al.   Genes

AciDB 1.0: A database of acidophilic organisms, their genomic information and associated metadata

(2020) Gonzalo Neira et al.   BIOINFORMATICS

Deciphering the functional diversity of DNA-binding transcription factors in Bacteria and Archaea organisms

(2020) Emanuel Flores-Bautista et al.   PLoS One

Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera

(2019) Tomohiro Watanabe et al.   Frontiers in Microbiology

Effect of CO2 Concentration on Uptake and Assimilation of Inorganic Carbon in the Extreme Acidophile Acidithiobacillus ferrooxidans

(2019) Mario Esparza et al.   Frontiers in Microbiology

Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans

(2019) Héctor Osorio et al.   Frontiers in Microbiology

Microbiomes in extremely acidic environments: functionalities and interactions that allow survival and growth of prokaryotes at low pH

(2018) Raquel Quatrini et al.   CURRENT OPINION IN MICROBIOLOGY

Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors

(2018) Ernesto Perez-Rueda et al.   PLoS One

Functional Prediction of Hypothetical Transcription Factors of Escherichia coli K-12 Based on Expression Data

(2018) Emanuel Flores-Bautista et al.   Computational and Structural Biotechnology Journal

The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver

(2018) Arun Prasad Pandurangan et al.   NUCLEIC ACIDS RESEARCH

Dissecting the protein architecture of DNA-binding transcription factors in bacteria and archaea

(2017) Nancy Rivera-Gómez et al.   MICROBIOLOGY-SGM

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

The Global Redox Responding RegB/RegA Signal Transduction System Regulates the Genes Involved in Ferrous Iron and Inorganic Sulfur Compound Oxidation of the Acidophilic Acidithiobacillus ferrooxidans

(2017) Danielle Moinier et al.   Frontiers in Microbiology

Molecular Systematics of the Genus Acidithiobacillus: Insights into the Phylogenetic Structure and Diversification of the Taxon

(2017) Harold Nuñez et al.   Frontiers in Microbiology

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Biomining of metals: how to access and exploit natural resource sustainably

(2017) Carlos A. Jerez   Microbial Biotechnology

The σ54-dependent two-component system regulating sulfur oxidization (Sox) system in Acidithiobacillus caldus and some chemolithotrophic bacteria

(2016) Li-Feng Li et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Acidithiobacillus ferriphilus sp. nov., a facultatively anaerobic iron- and sulfur-metabolizing extreme acidophile

(2016) Carmen Falagán et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

The Two-Component System RsrS-RsrR Regulates the Tetrathionate Intermediate Pathway for Thiosulfate Oxidation in Acidithiobacillus caldus

(2016) Zhao-Bao Wang et al.   Frontiers in Microbiology

Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics

(2016) Xian Zhang et al.   Frontiers in Microbiology

Insights into the Quorum Sensing Regulon of the Acidophilic Acidithiobacillus ferrooxidans Revealed by Transcriptomic in the Presence of an Acyl Homoserine Lactone Superagonist Analog

(2016) Sigde Mamani et al.   Frontiers in Microbiology

Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation

(2016) Carolina González et al.   Frontiers in Microbiology

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective

(2014) Andrey Feklístov et al.   Annual Review of Microbiology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities

(2014) Daniela S Aliaga Goltsman et al.   ISME Journal

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative Genomics of Transcriptional Regulation of Methionine Metabolism in Proteobacteria

(2014) Semen A. Leyn et al.   PLoS One

A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment

(2014) Dante Travisany et al.   RESEARCH IN MICROBIOLOGY

Bioinformatic Prediction of Gene Functions Regulated by Quorum Sensing in the Bioleaching Bacterium Acidithiobacillus ferrooxidans

(2013) Alvaro Banderas et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria

(2013) K. P. Williams et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Acidithiobacillus ferridurans sp. nov., an acidophilic iron-, sulfur- and hydrogen-metabolizing chemolithotrophic gammaproteobacterium

(2013) S. Hedrich et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Biodiversity, metabolism and applications of acidophilic sulfur-metabolizing microorganisms

(2012) Mark Dopson et al.   ENVIRONMENTAL MICROBIOLOGY

Genome wide identification of Acidithiobacillus ferrooxidans (ATCC 23270) transcription factors and comparative analysis of ArsR and MerR metal regulators

(2011) Christian Hödar et al.   BIOMETALS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

(2011) Dmitry A Rodionov et al.   BMC GENOMICS

Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications

(2009) Jorge Valdés et al.   BMC GENOMICS

Operons

(2009) Anne E. Osbourn et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Oxidation of elemental sulfur, tetrathionate and ferrous iron by the psychrotolerant Acidithiobacillus strain SS3

(2009) Daniel Kupka et al.   RESEARCH IN MICROBIOLOGY

Presence of a Family of Plasmids (29 to 65 Kilobases) with a 26-Kilobase Common Region in Different Strains of the Sulfur-Oxidizing Bacterium Acidithiobacillus caldus

(2008) L. J. van Zyl et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Glu43 is an essential residue for coordinating the [Fe2S2] cluster of IscR fromAcidithiobacillus ferrooxidans

(2008) Jia Zeng et al.   FEBS LETTERS

Comparative genome analysis of Acidithiobacillus ferrooxidans, A. thiooxidans and A. caldus: Insights into their metabolism and ecophysiology

(2008) Jorge Valdés et al.   HYDROMETALLURGY

The cis-regulatory map of Shewanella genomes

(2008) J. Liu et al.   NUCLEIC ACIDS RESEARCH