Comment on the position of nitrate respiration in metabolic evolution

Genes coding for enzymes of the denitrification pathway appear randomly distributed among isolates of the ancestral genus Thermus, but only in few strains of the species Thermus thermophilus has the pathway been studied to a certain detail. Here, we review the enzymes involved in this pathway present in T. thermophilus NAR1, a strain extensively employed as a model for nitrate respiration, in the light of its full sequence recently assembled through a combination of PacBio and Illumina technologies in order to counteract the systematic errors introduced by the former technique. The genome of this strain is divided in four replicons, a chromosome of 2,021,843 bp, two megaplasmids of 370,865 and 77,135 bp and a small plasmid of 9799 pb. Nitrate respiration is encoded in the largest megaplasmid, pTTHNP4, within a region that includes operons for O2 and nitrate sensory systems, a nitrate reductase, nitrate and nitrite transporters and a nitrate specific NADH dehydrogenase, in addition to multiple insertion sequences (IS), suggesting its mobility-prone nature. Despite nitrite is the final product of nitrate respiration in this strain, the megaplasmid encodes two putative nitrite reductases of the cd1 and Cu-containing types, apparently inactivated by IS. No nitric oxide reductase genes have been found within this region, although the NorR sensory gene, needed for its expression, is found near the inactive nitrite respiration system. These data clearly support that partial denitrification in this strain is the consequence of recent deletions and IS insertions in genes involved in nitrite respiration. Based on these data, the capability of this strain to transfer or acquire denitrification clusters by horizontal gene transfer is discussed.

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Metabolic evolution and the self-organization of ecosystems

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1619573114 ◽

2017 ◽

Vol 114 (15) ◽

pp. E3091-E3100 ◽

Cited By ~ 64

Author(s):

Rogier Braakman ◽

Michael J. Follows ◽

Sallie W. Chisholm

Keyword(s):

Organic Carbon ◽

Metabolic Rate ◽

Light Adaptation ◽

Atmospheric Oxygen ◽

Heterotrophic Bacterium ◽

The Self ◽

Self Organization ◽

Steady Increase ◽

Mathematical Framework ◽

Metabolic Evolution

Metabolism mediates the flow of matter and energy through the biosphere. We examined how metabolic evolution shapes ecosystems by reconstructing it in the globally abundant oceanic phytoplankterProchlorococcus. To understand what drove observed evolutionary patterns, we interpreted them in the context of its population dynamics, growth rate, and light adaptation, and the size and macromolecular and elemental composition of cells. This multilevel view suggests that, over the course of evolution, there was a steady increase inProchlorococcus’ metabolic rate and excretion of organic carbon. We derived a mathematical framework that suggests these adaptations lower the minimal subsistence nutrient concentration of cells, which results in a drawdown of nutrients in oceanic surface waters. This, in turn, increases total ecosystem biomass and promotes the coevolution of all cells in the ecosystem. Additional reconstructions suggest thatProchlorococcusand the dominant cooccurring heterotrophic bacterium SAR11 form a coevolved mutualism that maximizes their collective metabolic rate by recycling organic carbon through complementary excretion and uptake pathways. Moreover, the metabolic codependencies ofProchlorococcusand SAR11 are highly similar to those of chloroplasts and mitochondria within plant cells. These observations lead us to propose a general theory relating metabolic evolution to the self-amplification and self-organization of the biosphere. We discuss the implications of this framework for the evolution of Earth’s biogeochemical cycles and the rise of atmospheric oxygen.

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The complete denitrification pathway of the symbiotic, nitrogen-fixing bacterium Bradyrhizobium japonicum

Biochemical Society Transactions ◽

10.1042/bst0330141 ◽

2005 ◽

Vol 33 (1) ◽

pp. 141-144 ◽

Cited By ~ 102

Author(s):

E.J. Bedmar ◽

E.F. Robles ◽

M.J. Delgado

Keyword(s):

Nitric Oxide ◽

Nitrous Oxide ◽

Bradyrhizobium Japonicum ◽

Mutational Analysis ◽

Control Level ◽

Gene Clusters ◽

Alternative Form ◽

Nitrate Respiration ◽

Regulatory Cascade ◽

Denitrification Genes

Denitrification is an alternative form of respiration in which bacteria sequentially reduce nitrate or nitrite to nitrogen gas by the intermediates nitric oxide and nitrous oxide when oxygen concentrations are limiting. In Bradyrhizobium japonicum, the N2-fixing microsymbiont of soya beans, denitrification depends on the napEDABC, nirK, norCBQD, and nosRZDFYLX gene clusters encoding nitrate-, nitrite-, nitric oxide- and nitrous oxide-reductase respectively. Mutational analysis of the B. japonicum nap genes has demonstrated that the periplasmic nitrate reductase is the only enzyme responsible for nitrate respiration in this bacterium. Regulatory studies using transcriptional lacZ fusions to the nirK, norCBQD and nosRZDFYLX promoter region indicated that microaerobic induction of these promoters is dependent on the fixLJ and fixK2 genes whose products form the FixLJ–FixK2 regulatory cascade. Besides FixK2, another protein, nitrite and nitric oxide respiratory regulator, has been shown to be required for N-oxide regulation of the B. japonicum nirK and norCBQD genes. Thus nitrite and nitric oxide respiratory regulator adds to the FixLJ–FixK2 cascade an additional control level which integrates the N-oxide signal that is critical for maximal induction of the B. japonicum denitrification genes. However, the identity of the signalling molecule and the sensing mechanism remains unknown.

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Role ofBradyrhizobium japonicumcytochromec550in nitrite and nitrate respiration

FEMS Microbiology Letters ◽

10.1111/j.1574-6968.2007.01034.x ◽

2008 ◽

Vol 279 (2) ◽

pp. 188-194 ◽

Cited By ~ 15

Author(s):

Emilio Bueno ◽

Eulogio J. Bedmar ◽

David J. Richardson ◽

MarÃa J. Delgado

Keyword(s):

Nitrate Respiration

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In Silico Evolution of Early Metabolism

Artificial Life ◽

10.1162/artl_a_00021 ◽

2011 ◽

Vol 17 (2) ◽

pp. 87-108 ◽

Cited By ~ 8

Author(s):

Alexander Ullrich ◽

Markus Rohrschneider ◽

Gerik Scheuermann ◽

Peter F. Stadler ◽

Christoph Flamm

Keyword(s):

Metabolic Pathways ◽

Genetic System ◽

Simulation Tool ◽

Metabolic Evolution ◽

Metabolic System ◽

Evolution Of Metabolic Pathways ◽

Core Set ◽

Catalytically Active ◽

Almost Open ◽

In Silico Evolution

We developed a simulation tool for investigating the evolution of early metabolism, allowing us to speculate on the formation of metabolic pathways from catalyzed chemical reactions and on the development of their characteristic properties. Our model consists of a protocellular entity with a simple RNA-based genetic system and an evolving metabolism of catalytically active ribozymes that manipulate a rich underlying chemistry. Ensuring an almost open-ended and fairly realistic simulation is crucial for understanding the first steps in metabolic evolution. We show here how our simulation tool can be helpful in arguing for or against hypotheses on the evolution of metabolic pathways. We demonstrate that seemingly mutually exclusive hypotheses may well be compatible when we take into account that different processes dominate different phases in the evolution of a metabolic system. Our results suggest that forward evolution shapes metabolic network in the very early steps of evolution. In later and more complex stages, enzyme recruitment supersedes forward evolution, keeping a core set of pathways from the early phase.

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Comparative Genomics Provides Insights into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera

Genes ◽

10.3390/genes12010071 ◽

2021 ◽

Vol 12 (1) ◽

pp. 71

Author(s):

Roberto Tadeu Raittz ◽

Camilla Reginatto De Pierri ◽

Marta Maluk ◽

Marcelo Bueno Batista ◽

Manuel Carmona ◽

...

Keyword(s):

Aromatic Compounds ◽

Growth Promotion ◽

Nitrogenase Activity ◽

Full Length ◽

Polluted Water ◽

Nitrate Respiration ◽

Nif Genes ◽

Diverse Range ◽

Single Strain ◽

Group 2

Among other attributes, the Betaproteobacterial genus Azoarcus has biotechnological importance for plant growth-promotion and remediation of petroleum waste-polluted water and soils. It comprises at least two phylogenetically distinct groups. The “plant-associated” group includes strains that are isolated from the rhizosphere or root interior of the C4 plant Kallar Grass, but also strains from soil and/or water; all are considered to be obligate aerobes and all are diazotrophic. The other group (now partly incorporated into the new genus Aromatoleum) comprises a diverse range of species and strains that live in water or soil that is contaminated with petroleum and/or aromatic compounds; all are facultative or obligate anaerobes. Some are diazotrophs. A comparative genome analysis of 32 genomes from 30 Azoarcus-Aromatoleum strains was performed in order to delineate generic boundaries more precisely than the single gene, 16S rRNA, that has been commonly used in bacterial taxonomy. The origin of diazotrophy in Azoarcus-Aromatoleum was also investigated by comparing full-length sequences of nif genes, and by physiological measurements of nitrogenase activity using the acetylene reduction assay. Based on average nucleotide identity (ANI) and whole genome analyses, three major groups could be discerned: (i) Azoarcus comprising Az. communis, Az. indigens and Az. olearius, and two unnamed species complexes, (ii) Aromatoleum Group 1 comprising Ar. anaerobium, Ar. aromaticum, Ar. bremense, and Ar. buckelii, and (iii) Aromatoleum Group 2 comprising Ar. diolicum, Ar. evansii, Ar. petrolei, Ar. toluclasticum, Ar. tolulyticum, Ar. toluolicum, and Ar. toluvorans. Single strain lineages such as Azoarcus sp. KH32C, Az. pumilus, and Az. taiwanensis were also revealed. Full length sequences of nif-cluster genes revealed two groups of diazotrophs in Azoarcus-Aromatoleum with nif being derived from Dechloromonas in Azoarcus sensu stricto (and two Thauera strains) and from Azospira in Aromatoleum Group 2. Diazotrophy was confirmed in several strains, and for the first time in Az. communis LMG5514, Azoarcus sp. TTM-91 and Ar. toluolicum TT. In terms of ecology, with the exception of a few plant-associated strains in Azoarcus (s.s.), across the group, most strains/species are found in soil and water (often contaminated with petroleum or related aromatic compounds), sewage sludge, and seawater. The possession of nar, nap, nir, nor, and nos genes by most Azoarcus-Aromatoleum strains suggests that they have the potential to derive energy through anaerobic nitrate respiration, so this ability cannot be usefully used as a phenotypic marker to distinguish genera. However, the possession of bzd genes indicating the ability to degrade benzoate anaerobically plus the type of diazotrophy (aerobic vs. anaerobic) could, after confirmation of their functionality, be considered as distinguishing phenotypes in any new generic delineations. The taxonomy of the Azoarcus-Aromatoleum group should be revisited; retaining the generic name Azoarcus for its entirety, or creating additional genera are both possible outcomes.

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The contribution of nitrate respiration to the energy budget of the symbiont-containing clam Lucinoma aequizonata: a calorimetric study

Journal of Experimental Biology ◽

10.1242/jeb.199.2.427 ◽

1996 ◽

Vol 199 (2) ◽

pp. 427-433

Author(s):

U Hentschel ◽

S Hand ◽

H Felbeck

Keyword(s):

Heat Production ◽

Sea Water ◽

Anaerobic Respiration ◽

Gill Tissue ◽

Nitrate Respiration ◽

Heat Output ◽

Marine Bivalve ◽

Calorimetric Study ◽

Perfusion Medium ◽

Terminal Electron Acceptor

Heat production and nitrate respiration rates were measured simultaneously in the gill tissue of Lucinoma aequizonata. This marine bivalve contains chemoautotrophic, intracellular, bacterial symbionts in its gill tissue. The symbionts show constitutive anaerobic respiration, using nitrate instead of oxygen as a terminal electron acceptor. An immediate increase in heat production was observed after the addition of nitrate to the perfusion medium of the calorimeter and this was accompanied by the appearance of nitrite in the effluent sea water. The nitrate-stimulated heat output was similar under aerobic and anaerobic conditions, which is consistent with the constitutive nature of nitrate respiration. The amount of heat released was dependent on the concentration of nitrate in the perfusion medium. At nitrate concentrations between 0.5 and 5 mmol l-1, the total heat production was increased over twofold relative to unstimulated baseline values. A mean (±s.e.m.) experimental enthalpy of -130±22.6 kJ mol-1 nitrite (N=13) was measured for this concentration range.

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