Ancestral hemoglobins in
            <i>Archaea</i>

Freitas, Tracey; Hou, Shaobin; Dioum, Elhadji M.; Saito, Jennifer A.; Newhouse, James S.; González, Gonzalo; Gilles-Gonzalez, Marie Alda; Alam, Maqsudul

doi:10.1073/pnas.0308657101

Cited by 98 publications

(91 citation statements)

References 41 publications

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“…Structural studies have shown that heme ligand in Hmp is stabilized by His-85, Tyr-29, and Gln-53 (13). The proximal F8 histidine (His-85 in Salmonella Hmp) in the heme pocket was found to be absolutely conserved in an alignment of 700 vertebrate and nonvertebrate globins and shown to be essential for heme binding in the protoglobin of Aeropyrum pernix (57). In this study an H85A mutation was found to abolish NO⅐ detoxification (Fig.…”

Section: Discussionmentioning

confidence: 83%

Maintenance of Nitric Oxide and Redox Homeostasis by the Salmonella Flavohemoglobin Hmp

Bang

Liu

Vázquez‐Torres

et al. 2006

Journal of Biological Chemistry

169

191

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Intracellular pathogens must resist the antimicrobial actions of nitric oxide (NO⅐) produced by host cells. To this end pathogens possess several NO⅐-metabolizing enzymes. Here we show that the flavohemoglobin Hmp is the principal enzyme responsible for aerobic NO⅐ metabolism by Salmonella enterica serovar typhimurium. We further show that Hmp is required for Salmonella virulence in mice, in contrast to S-nitrosoglutathione reductase, flavorubredoxin, or cytochrome c nitrite reductase. Abrogation of murine-inducible NO⅐ synthase restores virulence to hmp mutant bacteria. In the presence of nitrosative stress, Hmp-deficient Salmonella exhibits reduced NO⅐ consumption, impaired growth, increased protein S-nitrosylation, and filamentous morphology. However, under aerobic conditions in the absence of nitrosative stress, elevated hmp expression increases S. typhimurium susceptibility to hydrogen peroxide. Both the heme binding and flavoreductase domains are required for resistance to NO⅐, whereas the flavoreductase domain is responsible for iron-dependent susceptibility to oxidative stress. This provides a rationale for the regulation of hmp expression by the transcriptional repressor NsrR in response to both nitrosative stress and intracellular free iron concentration. The Hmp flavohemoglobin plays a central role in the response of Salmonella to nitrosative stress but requires precise regulation to avoid the exacerbation of oxidative stress that can result if electrons are shuttled to extraneous iron.

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Section: Discussionmentioning

confidence: 83%

Maintenance of Nitric Oxide and Redox Homeostasis by the Salmonella Flavohemoglobin Hmp

Bang

Liu

Vázquez‐Torres

et al. 2006

Journal of Biological Chemistry

169

191

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“…Specifically, the NAG1 contains the most deeply rooted protoglobin known to date (Supplementary Figure S8), and appears to provide an evolutionary linkage to higher globins such as hemoglobin that are thought to have evolved from an ancestral protoglobin (Moens et al, 1996;Freitas et al, 2005;Nardini et al, 2008). Protoglobins from the obligately aerobic hyperthermophile A. pernix and the strictly anaerobic methanogen Methanosarcina acetivorans have been found to bind molecular oxygen, nitric oxide and CO, potentially protecting the organisms from nitrosative and oxidative stress (Freitas et al, 2004). Consequently, protoglobins have been found in both aerobic and anaerobic organisms.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, the NAG1 sequence is the most deeply rooted entry of all known globins/protoglobins (Supplementary Figure S8). The protein sequence is related to characterized protoglobins in Aeropyrum pernix, which suggests possible involvement in binding O 2 , CO and NO (Freitas et al, 2004). Other genes encoding proteins for heavy metal detoxification and reduction of oxidative stress are found in the NAG1 assembly and include mercuric reductase (merA), arsenic resistance (arsABC), a superoxide dismutase (sodA) and multiple peroxiredoxins.…”

Section: Functional Analysis Of Nag1 Genome Sequencementioning

confidence: 99%

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

et al. 2012

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Geothermal systems in Yellowstone National Park (YNP) provide an outstanding opportunity to understand the origin and evolution of metabolic processes necessary for life in extreme environments including low pH, high temperature, low oxygen and elevated concentrations of reduced iron. Previous phylogenetic studies of acidic ferric iron mats from YNP have revealed considerable diversity of uncultivated and undescribed archaea. The goal of this study was to obtain replicate de novo genome assemblies for a dominant archaeal population inhabiting acidic ironoxide mats in YNP. Detailed analysis of conserved ribosomal and informational processing genes indicates that the replicate assemblies represent a new candidate phylum within the domain Archaea referred to here as 'Geoarchaeota' or 'novel archaeal group 1 (NAG1)'. The NAG1 organisms contain pathways necessary for the catabolism of peptides and complex carbohydrates as well as a bacterial-like Form I carbon monoxide dehydrogenase complex likely used for energy conservation. Moreover, this novel population contains genes involved in the metabolism of oxygen including a Type A heme copper oxidase, a bd-type terminal oxidase and a putative oxygen-sensing protoglobin. NAG1 has a variety of unique bacterial-like cofactor biosynthesis and transport genes and a Type3-like CRISPR system. Discovery of NAG1 is critical to our understanding of microbial community structure and function in extant thermophilic iron-oxide mats of YNP, and will provide insight regarding the evolution of Archaea in early Earth environments that may have important analogs active in YNP today.

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“…A class of generegulating, chimeric heme proteins, the globin-coupled sensors (GCSs), was discovered in several bacterial groups and an archaean (21). The related single-domain protoglobins (Pgbs) found in archea and bacteria have been proposed to represent the ''ancestral'' globin (22). Here, we report the results of a comprehensive survey of globins.…”

mentioning

confidence: 99%

Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life

Vinogradov

Hoogewijs

Bailly

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

154

132

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Although most globins, including the N-terminal domains within chimeric proteins such as flavohemoglobins and globin-coupled sensors, exhibit a 3͞3 helical sandwich structure, many bacterial, plant, and ciliate globins have a 2͞2 helical sandwich structure. We carried out a comprehensive survey of globins in the genomes from the three kingdoms of life. Bayesian phylogenetic trees based on manually aligned sequences indicate the possibility of past horizontal globin gene transfers from bacteria to eukaryotes. BLASTP searches revealed the presence of 3͞3 single-domain globins related to the globin domains of the bacterial and fungal flavohemoglobins in many bacteria, a red alga, and a diatom. Iterated PSI-BLAST searches based on groups of globin sequences found that only the single-domain globins and flavohemoglobins recognize the eukaryote 3͞3 globins, including vertebrate neuroglobins, ␣-and ␤-globins, and cytoglobins. The 2͞2 globins recognize the flavohemoglobins, as do the globin coupled sensors and the closely related single-domain protoglobins. However, the 2͞2 globins and the globin-coupled sensors do not recognize each other. Thus, all globins appear to be distributed among three lineages: (i) the 3͞3 plant and metazoan globins, single-domain globins, and flavohemoglobins; (ii) the bacterial 3͞3 globin-coupled sensors and protoglobins; and (iii) the bacterial, plant, and ciliate 2͞2 globins. The three lineages may have evolved from an ancestral 3͞3 or 2͞2 globin. Furthermore, it appears likely that the predominant functions of globins are enzymatic and that oxygen transport is a specialized development that accompanied the evolution of metazoans.evolution ͉ sequences T hirty years ago, our knowledge of globin sequences was limited to vertebrate ␣-and ␤-globins, myoglobins (Mbs), and the symbiotic Hbs of legume plants. The ensuing years brought the discovery of 3͞3 nonsymbiotic plant Hbs (NsHbs) in plants, symbiotic Hbs in plants other than legumes, and chimeric f lavohemoglobins (FHbs), which are comprised of an Nterminal globin linked to an FAD reductase domain, in bacteria and yeasts (1-8). Concurrently, globins shorter than normal (Ͻ130 aa), the ''truncated'' Hbs, were observed in protozoa and bacteria (9, 10), and globins longer than normal (Ͼ150 aa), which aligned with the truncated Hbs, were found in green alga (11) and plants (12). The crystal structures of these globins (13-15) exhibited a novel globin fold comprised of a 2͞2 helical sandwich secondary structure. The recent rapid accumulation of genomic information has resulted in the discoveries of new types of globins, including the 3͞3 neuroglobins (Ngbs) and 3͞3 cytoglobins (Cygbs) believed to occur in all vertebrates (16), and of globins in organisms in which their presence had not been suspected, such as nematodes (17), an insect (18), and a urochordate (19). Furthermore, genomic data brought to light the existence of 3͞3 single-domain globins (SDgbs), which aligned with the globin domain of the FHbs (20). A class of generegulating, chimeric...

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Ancestral hemoglobins in Archaea

Cited by 98 publications

References 41 publications

Maintenance of Nitric Oxide and Redox Homeostasis by the Salmonella Flavohemoglobin Hmp

Maintenance of Nitric Oxide and Redox Homeostasis by the Salmonella Flavohemoglobin Hmp

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life

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