Ribulose bisphosphate carboxylase activity and a Calvin cycle gene cluster in Sulfobacillus species

Caldwell, Paul E.; MacLean, Martin R.; Norris, Paul R.

doi:10.1099/mic.0.2007/006262-0

Cited by 35 publications

(24 citation statements)

References 45 publications

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“…Sulfobacillus spp. are known as mixotrophic acidophiles that are capable of assimilating organic and inorganic carbon (30,34,42,51). Similar to the published Sulfobacillus genomes (30, 31), a full suite of genes involved in the Calvin-Benson-Bassham cycle were predicted in all strains ( Fig.…”

Section: Figsupporting

confidence: 59%

Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss

Zhang

Liu

Liang

et al. 2017

Appl Environ Microbiol

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Recent phylogenomic analysis has suggested that three strains isolated from different copper mine tailings around the world were taxonomically affiliated with Sulfobacillus thermosulfidooxidans. Here, we present a detailed investigation of their genomic features, particularly with respect to metabolic potentials and stress tolerance mechanisms. Comprehensive analysis of the Sulfobacillus genomes identified a core set of essential genes with specialized biological functions in the survival of acidophiles in their habitats, despite differences in their metabolic pathways. The Sulfobacillus strains also showed evidence for stress management, thereby enabling them to efficiently respond to harsh environments. Further analysis of metabolic profiles provided novel insights into the presence of genomic streamlining, highlighting the importance of gene loss as a main mechanism that potentially contributes to cellular economization. Another important evolutionary force, especially in larger genomes, is gene acquisition via horizontal gene transfer (HGT), which might play a crucial role in the recruitment of novel functionalities. Also, a successful integration of genes acquired from archaeal donors appears to be an effective way of enhancing the adaptive capacity to cope with environmental changes. Taken together, the findings of this study significantly expand the spectrum of HGT and genome reduction in shaping the evolutionary history of Sulfobacillus strains.IMPORTANCE Horizontal gene transfer (HGT) and gene loss are recognized as major driving forces that contribute to the adaptive evolution of microbial genomes, although their relative importance remains elusive. The findings of this study suggest that highly frequent gene turnovers within microorganisms via HGT were necessary to incur additional novel functionalities to increase the capacity of acidophiles to adapt to changing environments. Evidence also reveals a fascinating phenomenon of potential cross-kingdom HGT. Furthermore, genome streamlining may be a critical force in driving the evolution of microbial genomes. Taken together, this study provides insights into the importance of both HGT and gene loss in the evolution and diversification of bacterial genomes.

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Section: Figsupporting

confidence: 59%

Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss

Zhang

Liu

Liang

et al. 2017

Appl Environ Microbiol

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“…Besides cyanobacteria, the CBB cycle occurs in photo-and (aerobic) chemoautotrophic Alpha-, Beta-, and Gammaproteobacteria. In addition, some Gram-positives (Sulfobacillus spp., Firmicutes) and members of the Oscillochloridaceae (Chloroflexi) use this cycle (Caldwell et al 2007, Ivanovsky et al 1999.…”

Section: Calvin-benson-bassham Cyclementioning

confidence: 99%

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

Hügler

Sievert

2011

Annu. Rev. Mar. Sci.

545

486

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Organisms capable of autotrophic metabolism assimilate inorganic carbon into organic carbon. They form an integral part of ecosystems by making an otherwise unavailable form of carbon available to other organisms, a central component of the global carbon cycle. For many years, the doctrine prevailed that the Calvin-Benson-Bassham (CBB) cycle is the only biochemical autotrophic CO2 fixation pathway of significance in the ocean. However, ecological, biochemical, and genomic studies carried out over the last decade have not only elucidated new pathways but also shown that autotrophic carbon fixation via pathways other than the CBB cycle can be significant. This has ramifications for our understanding of the carbon cycle and energy flow in the ocean. Here, we review the recent discoveries in the field of autotrophic carbon fixation, including the biochemistry and evolution of the different pathways, as well as their ecological relevance in various oceanic ecosystems.

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“…The CB cycle operates in plants, algae, cyanobacteria, and many aerobic or facultative aerobic proteobacteria belonging to the alpha, beta, and gamma subgroups. It was also shown for Sulfobacillus spp., iron and sulfur-oxidizing members of the firmicutes (19,129), some mycobacteria (65), and green nonsulfur bacteria of the genus Oscillochloris (phylum Chloroflexi) (12,51). The CB cycle not only functions in autotrophic CO 2 fixation but is also required as an electron sink for (anaerobic) photoheterotrophic growth of some purple bacteria (e.g., Rhodobacter, Rhodospirillum, and Rhodopseudomonas) on substrates, which are more reduced than the average cell carbon (54,118).…”

Section: Route 1: the Calvin-benson Reductive Pentose Phosphate Cyclementioning

confidence: 99%

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

Berg

2011

Appl Environ Microbiol

692

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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Ribulose bisphosphate carboxylase activity and a Calvin cycle gene cluster in Sulfobacillus species

Cited by 35 publications

References 45 publications

Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss

Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

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

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Ribulose bisphosphate carboxylase activity and a Calvin cycle gene cluster in Sulfobacillus species

Cited by 35 publications

References 45 publications

Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss

Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

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

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