Selenium-dependent gene expression in Methanococcus maripaludis: Involvement of the transcriptional regulator HrsM

Quitzke, Vivien; Fersch, Julia; Seyhan, Deniz; Rother, Michael

doi:10.1016/j.bbagen.2018.03.030

Cited by 11 publications

(35 citation statements)

References 52 publications

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“…Table 1 shows several examples of LTTRs to show the CbnR Chlorocatechol catabolism (2-chloro-) cis, cis-muconate Cupriavidus necator ClcR Chlorocatechol catabolism 2-chloro-cis, cis-muconate Pseudomonas putida Coco et al, 1993 CrgA Biosynthesis of pili and capsule -methylene--butyrolactone Neisseria meningitidis Deghmane et al, 2000 CysB L-Cysteine synthesis N-acetylserine Salmonella typhimurium Kredlich, 1971 DntR 2,4-Dinitrotoluene 2,4-dinitrotoluene, salicylate Burkholderia sp. Smirnova et al, 2004 FinR Ferredoxin-NADP + reductase oxidative and osmotic stresses Pseudomonas putida Lee et al, 2006 HrsM Expression of selenoproteins involved in energy metabolism and methanogenesis Unknown Methanococcus maripaludis Quitzke et al, 2018 IlvY Synthesis of isoleucine and valine -acetohydroxybutyrate, -acetolactate Escherichia coli Wek and Hatfield, 1988 LdhR Cellular aggregates and biofilm formation Unknown Bukholderia multivorans Silva et al, 2018 LeuO Leucine synthesis, environmental adaptation and virulence Unknown Salmonella typhimurium, Escherichia coli Hertzberg et al, 1980 LysR Lysine synthesis diaminopimelate Escherichia coli Stragier et al, 1983 MetR Synthesis and transport of methionine and cysteine homocysteine…”

Section: Introductionmentioning

confidence: 99%

STRUCTURAL STUDIES OF TRANSCRIPTIONAL REGULATION BY LysR-TYPE TRANSCRIPTIONAL REGULATORS IN BACTERIA

Koentjoro

Ogawa

2018

RAS

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LysR-type transcriptional regulators (LTTRs) comprise one of the largest families of transcriptional regulators in bacteria andcontrol gene expression of various types of metabolic, virulence and physiological functions. LTTRs typically form homotetramers and require an inducer molecule(s) to activate the transcription of target genes. The N-terminal region of LTTRs contains a DNAbinding domain (DBD) with the winged helix-turn-helix motif that specifically binds the promoter region of target genes. The C-terminal region of LTTRs is connected to the DBD by a linker helix and forms the regulatory domain (RD) that contains a binding pocket for inducer molecules. Crystal structures of several LTTR family members together with their biochemical analyses have provided a potential mechanism for the initial process of transcriptional activation by LTTRs. First, helix 3 of the winged helix-turn-helix motif in DBD is supposed to distinguish the recognition binding site (RBS) in the promoter region, resulting in complex formation through interactions between two DBDs in the tetrameric LTTR and RBS. Formation of this complex seems to enable interactions between the other two DBDs in the LTTR tetramer and the activation binding site (ABS) in the promoter region.The binding of the tetrameric LTTR to both the RBS and ABS causes the promoter DNA to adopt a bent structure because the four DBDs in the tetrameric LTTR are arranged in a V-shaped manner at the bottom of the LTTR. Interaction of an inducer molecule(s) with the RD seems to cause a quaternary structural change of the LTTR that relaxes the bending angle of the promoter DNA with a concomitant shift of the bound DBDs at the ABS. These events facilitate recruitment of RNA polymerase to its binding site in the promoter region, which overlaps with the ABS for LTTR.

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Section: Introductionmentioning

confidence: 99%

STRUCTURAL STUDIES OF TRANSCRIPTIONAL REGULATION BY LysR-TYPE TRANSCRIPTIONAL REGULATORS IN BACTERIA

Koentjoro

Ogawa

2018

RAS

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“…By using comparative genomic approaches in the field of trace elements, we may better understand trace element-dependent cellular processes and proteins that an organism has [ 71 , 72 ]. To date, several comparative genomic studies have analyzed the distribution and evolutionary trends of Se metabolic pathways and/or selenoproteins in a variety of bacteria and archaea, which allow for a general understanding of the status of Se metabolism and function in the two kingdoms [ 46 , 47 , 65 , 73 , 74 , 75 , 76 , 77 , 78 ].…”

Section: Comparative Genomics Of Selenium Utilization In Prokaryotesmentioning

confidence: 99%

“…Based on the sequence and phylogenetic analyses of their neighboring genes, several new gene products were predicted to be involved in Se metabolism, including YedE (a possible Se-related transporter), YedF (a protein involved in Se-related redox processes), DUF3343-containing protein (a possible chaperon involved in Se trafficking), and LysR_Se (a Se-specific transcriptional regulator), which might be useful for a further understanding of the mechanism underlying the metabolism and homeostasis of Se in prokaryotes. Some of these genes, such as LysR_Se (or named HrsM), have been later experimentally verified [ 76 ].…”

Section: Comparative Genomics Of Selenium Utilization In Prokaryotesmentioning

confidence: 99%

Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective

et al. 2022

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Selenium (Se) is an important trace element that mainly occurs in the form of selenocysteine in selected proteins. In prokaryotes, Se is also required for the synthesis of selenouridine and Se-containing cofactor. A large number of selenoprotein families have been identified in diverse prokaryotic organisms, most of which are thought to be involved in various redox reactions. In the last decade or two, computational prediction of selenoprotein genes and comparative genomics of Se metabolic pathways and selenoproteomes have arisen, providing new insights into the metabolism and function of Se and their evolutionary trends in bacteria and archaea. This review aims to offer an overview of recent advances in bioinformatics analysis of Se utilization in prokaryotes. We describe current computational strategies for the identification of selenoprotein genes and generate the most comprehensive list of prokaryotic selenoproteins reported to date. Furthermore, we highlight the latest research progress in comparative genomics and metagenomics of Se utilization in prokaryotes, which demonstrates the divergent and dynamic evolutionary patterns of different Se metabolic pathways, selenoprotein families, and selenoproteomes in sequenced organisms and environmental samples. Overall, bioinformatics analyses of Se utilization, function, and evolution may contribute to a systematic understanding of how this micronutrient is used in nature.

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“…To identify genes important for natural transformation in M. maripaludis, we employed random transposon mutagenesis to screen for mutants with a transformation defect. In our hands, previous methods for generating transposon mutants were either low efficiency, labor intensive, or irreproducible (22)(23)(24). Thus, we sought to optimize the methods of Sattler et al and Quitzke et al (22,23) to improve efficiency.…”

Section: Optimizing M Maripaludis Mini-mariner Transposon Mutagenesismentioning

confidence: 99%

“…In our hands, previous methods for generating transposon mutants were either low efficiency, labor intensive, or irreproducible (22)(23)(24). Thus, we sought to optimize the methods of Sattler et al and Quitzke et al (22,23) to improve efficiency. Using HimarI transposase and a mini-mariner transposon (25), we incubated transposon DNA with at least a 2-fold stoichiometric excess of purified transposase before transfer into M. maripaludis via the polyethylene glycol (PEG) method of transformation (26).…”

Section: Optimizing M Maripaludis Mini-mariner Transposon Mutagenesismentioning

confidence: 99%

Random transposon mutagenesis identifies genes essential for transformation in naturally competent archaea

Fonseca

Loppnow

Day

et al. 2022

Preprint

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Natural transformation, the process whereby a cell acquires DNA directly from the environment, is an important driver of evolution in microbial populations. While transformation is well characterized in bacteria, relatively little is known about this process in archaea. Here, we leverage an optimized method to generate transposon mutants in Methanococcus maripaludis to screen for genes essential to natural transformation. A screen of 5,376 mutant strains identified 25 candidate genes. Among these are genes encoding components of the type IV-like pilus, transcription/translation associated genes, putative membrane bound transport proteins, and genes of unknown function. Interestingly, similar genes were identified regardless of whether replicating or integrating plasmids were provided as substrate for transformation. Using allelic replacement mutagenesis, we confirmed that several genes identified in these screens are essential for transformation. Finally, we identified a homolog of a membrane bound substrate transporter in Methanoculleus thermophilus and verified its importance using allelic replacement mutagenesis, suggesting a conserved mechanism for DNA transfer in multiple archaea. These data provide an initial catalog of genes important for transformation in the archaea and can inform efforts to understand gene flow in this domain.ImportanceHorizontal gene transfer (HGT) is an important driver of evolution in microbial populations. One of the primary ways microorganisms acquire genetic material through HGT is transformation, the direct uptake of DNA from the environment. While transformation is well-studied in bacteria, little is known about this process in archaea. Using a random mutagenesis screen to identify components of the archaeal transformation pathway, we identify a catalog of genes important to transformation in Methanococcus maripaludis and show that a subset of these genes is functionally conserved across diverse archaea. This is a key step in understanding mechanisms of gene flow in natural populations, and identification of the DNA uptake system will assist in establishing new model genetic systems for studying the archaea.

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Selenium-dependent gene expression in Methanococcus maripaludis: Involvement of the transcriptional regulator HrsM

Cited by 11 publications

References 52 publications

STRUCTURAL STUDIES OF TRANSCRIPTIONAL REGULATION BY LysR-TYPE TRANSCRIPTIONAL REGULATORS IN BACTERIA

STRUCTURAL STUDIES OF TRANSCRIPTIONAL REGULATION BY LysR-TYPE TRANSCRIPTIONAL REGULATORS IN BACTERIA

Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective

Random transposon mutagenesis identifies genes essential for transformation in naturally competent archaea

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