Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations

Levicán, Gloria; Ugalde, Juan A.; Ehrenfeld, Nicole; Maass, Alejandro; Parada, Pilar

doi:10.1186/1471-2164-9-581

Cited by 104 publications

(108 citation statements)

References 116 publications

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“…To our knowledge, this is the first report of this pathway in 'Ca. Magnetobacterium' genus, which is different from all known autotrophic members in Nitrospirae as well as MTB in Proteobacteria that conduct either rTCA cycle or Calvin-Benson-Bassham pathway for CO 2 fixation (Garrity and Holt, 2001;Matsunaga et al, 2005;Williams et al, 2006;Richter et al, 2007;Levican et al, 2008;Goltsman et al, 2009;Lucker et al, 2010;Ji et al, 2014). Compared with rTCA and Calvin-Benson-Bassham, the WL pathway is biochemically simple and energetically favorable (Peretó et al, 1999), which may lead to a growth advantage of these microorganisms in oxygen-limited environments.…”

Section: Discussionmentioning

confidence: 99%

Genomic insights into the uncultured genus ‘Candidatus Magnetobacterium’ in the phylum Nitrospirae

et al. 2014

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Magnetotactic bacteria (MTB) of the genus 'Candidatus Magnetobacterium' in phylum Nitrospirae are of great interest because of the formation of hundreds of bullet-shaped magnetite magnetosomes in multiple bundles of chains per cell. These bacteria are worldwide distributed in aquatic environments and have important roles in the biogeochemical cycles of iron and sulfur. However, except for a few short genomic fragments, no genome data are available for this ecologically important genus, and little is known about their metabolic capacity owing to the lack of pure cultures. Here we report the first draft genome sequence of 3.42 Mb from an uncultivated strain tentatively named 'Ca. Magnetobacterium casensis' isolated from Lake Miyun, China. The genome sequence indicates an autotrophic lifestyle using the Wood-Ljungdahl pathway for CO 2 fixation, which has not been described in any previously known MTB or Nitrospirae organisms. Pathways involved in the denitrification, sulfur oxidation and sulfate reduction have been predicted, indicating its considerable capacity for adaptation to variable geochemical conditions and roles in local biogeochemical cycles. Moreover, we have identified a complete magnetosome gene island containing mam, mad and a set of novel genes (named as man genes) putatively responsible for the formation of bullet-shaped magnetite magnetosomes and the arrangement of multiple magnetosome chains. This first comprehensive genomic analysis sheds light on the physiology, ecology and biomineralization of the poorly understood 'Ca. Magnetobacterium' genus.

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Section: Discussionmentioning

confidence: 99%

Genomic insights into the uncultured genus ‘Candidatus Magnetobacterium’ in the phylum Nitrospirae

et al. 2014

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“…77, 201177, MINIREVIEW 1927 it was found in anaerobic or microaerobic members of various other phyla such as Aquificae (11,49,92), Proteobacteria (especially of the delta and epsilon subdivisions) (20,48,70,89,104,122), and Nitrospirae (e.g., Nitrospira and Leptospirillum) (38,66,69). This cycle may in fact be widespread among anaerobic or microaerobic bacteria, but until now it had not been found in the archaeal domain (14,81).…”

Section: Route 2: the Reductive Citric Acid Cycle (Arnon-buchanan Cycle)mentioning

confidence: 99%

“…Citryl-CoA synthetase and citryl-CoA lyase are, however, phylogenetically related to ATP-citrate lyase (4,5,49). They were found in representatives of Aquificaceae (but not in other Aquificae) (4,5,49) and proposed for Leptospirillum (66). Furthermore, some proteobacteria (e.g., Magnetococcus sp.…”

Section: Route 2: the Reductive Citric Acid Cycle (Arnon-buchanan Cycle)mentioning

confidence: 99%

Ecological Aspects of the Distribution of Different Autotrophic CO ₂ Fixation Pathways

Berg

2011

Appl Environ Microbiol

666

589

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Autotrophic CO 2 fixation represents the most important biosynthetic process in biology. Besides the wellknown Calvin-Benson cycle, five other totally different autotrophic mechanisms are known today. This minireview discusses the factors determining their distribution. As will be made clear, the observed diversity reflects the variety of the organisms and the ecological niches existing in nature.Autotrophic CO 2 fixation represents the most important biosynthetic process in nature, being responsible for the net fixation of 7 ϫ 10 16 g carbon annually, corresponding to the conservation of 2.8 ϫ 1018 kJ of energy (107). The photosynthetic path of carbon in algae and plants was elucidated in the laboratory of Melvin Calvin in the 1940s and 1950s; the discovered reductive pentose phosphate (Calvin-Benson [CB]) cycle was immediately proposed to be the universal autotrophic carbon dioxide assimilation pathway, and the presence of its key enzyme, ribulose-1,5-bisphosphate carboxylase, was regarded as a synonym for autotrophy. This idea fit perfectly with the central biological dogma of that time, the biochemical unity of life (74). However, already in 1966 the second autotrophic CO 2 fixation cycle (the reductive citric acid cycle) had been discovered in the laboratory of Daniel Arnon (33). Today, six autotrophic CO 2 fixation mechanisms are known, raising the question of why so many pathways are necessary. In this review, the factors determining their distribution are discussed. As will be made clear, the observed diversity reflects the variety of the organisms and the ecological niches existing in nature. First, the general aspects of autotrophic CO 2 fixation will be discussed; then the known pathways will be introduced in the order of their discovery, highlighting their main characteristic features; finally, the main factors determining their distribution will be summarized. For those interested in a more detailed discussion of different aspects of autotrophy, several highly valuable reviews published in the last few years can be recommended, covering the function, structure, and evolution of ribulose-1,5-bisphosphate carboxylase (7,(101)(102)(103)111) and carboxysomes (61, 126); the reductive acetyl coenzyme A (acetyl-CoA) pathway (25,78,80) and the reductive citric acid cycle (2); CO 2 fixation in Archaea (14) and in deep-sea vent chemoautotrophs (73); and autotrophy in various oceanic ecosystems (47). GENERAL ASPECTS OF AUTOTROPHIC CO 2 FIXATIONIn general terms, the assimilation of CO 2 (oxidation state of ϩ4) into cellular carbon (average oxidation state of 0, as in carbohydrates) requires four reducing equivalents. An input of energy is also required for the reductive conversion of CO 2 to cell carbon and is provided by ATP hydrolysis. Anaerobes often use low-potential electron donors like reduced ferredoxin for CO 2 fixation, whereas aerobes usually rely on NAD(P)H as a reductant. Since reduced ferredoxin bears more energy than NADPH (ferredoxin, E 0 Ј Ϸ Ϫ400 mV; NADPH, E 0 Ј ϭ Ϫ320 mV), aerobic pathways usu...

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“…Furthermore, genes of the two-component nitrogen regulatory system in L. ferrooxidans C2-3 were identified: not only ntrCB but also nrtXY genes. ntrXY genes were also found in the complete genome sequence of Leptospirillum ferriphilum, which has not been deposited (5). Additionally, L. ferrooxidans C2-3 has some hydrogenase-encoding genes, which are considered to have potential for hydrogen oxidation.…”

mentioning

confidence: 96%

Complete Genome Sequence of Leptospirillum ferrooxidans Strain C2-3, Isolated from a Fresh Volcanic Ash Deposit on the Island of Miyake, Japan

et al. 2012

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Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations

Cited by 104 publications

References 116 publications

Genomic insights into the uncultured genus ‘Candidatus Magnetobacterium’ in the phylum Nitrospirae

Genomic insights into the uncultured genus ‘Candidatus Magnetobacterium’ in the phylum Nitrospirae

Ecological Aspects of the Distribution of Different Autotrophic CO ₂ Fixation Pathways

Complete Genome Sequence of Leptospirillum ferrooxidans Strain C2-3, Isolated from a Fresh Volcanic Ash Deposit on the Island of Miyake, Japan

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Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations

Cited by 104 publications

References 116 publications

Genomic insights into the uncultured genus ‘Candidatus Magnetobacterium’ in the phylum Nitrospirae

Genomic insights into the uncultured genus ‘Candidatus Magnetobacterium’ in the phylum Nitrospirae

Ecological Aspects of the Distribution of Different Autotrophic CO 2 Fixation Pathways

Complete Genome Sequence of Leptospirillum ferrooxidans Strain C2-3, Isolated from a Fresh Volcanic Ash Deposit on the Island of Miyake, Japan

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Ecological Aspects of the Distribution of Different Autotrophic CO ₂ Fixation Pathways