Response of cbb gene transcription levels of four typical sulfur-oxidizing bacteria to the CO 2 concentration and its effect on their carbon fixation efficiency during sulfur oxidation

Wang, Yanan; Wang, Lei; Tsang, Yiu Fai; Fu, Xiaohua; Hu, Jiajun; Li, Huan; Le, Yiquan

doi:10.1016/j.enzmictec.2016.06.015

Cited by 19 publications

(10 citation statements)

References 38 publications

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“…Some of these genomes have interesting metabolic or physiological properties, like a high trophic versatility in the sulfur-oxidizing α-proteobacterium Starkeya novella DSM 506 ( Kappler et al. 2001 , 2012 ; Wang et al. 2016 ), suggestive of LGT affecting that genome.…”

Section: Resultsmentioning

confidence: 99%

Bipartite Network Analysis of Gene Sharings in the Microbial World

Corel

Méheust

Watson

et al. 2018

Molecular Biology and Evolution

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Extensive microbial gene flows affect how we understand virology, microbiology, medical sciences, genetic modification, and evolutionary biology. Phylogenies only provide a narrow view of these gene flows: plasmids and viruses, lacking core genes, cannot be attached to cellular life on phylogenetic trees. Yet viruses and plasmids have a major impact on cellular evolution, affecting both the gene content and the dynamics of microbial communities. Using bipartite graphs that connect up to 149,000 clusters of homologous genes with 8,217 related and unrelated genomes, we can in particular show patterns of gene sharing that do not map neatly with the organismal phylogeny. Homologous genes are recycled by lateral gene transfer, and multiple copies of homologous genes are carried by otherwise completely unrelated (and possibly nested) genomes, that is, viruses, plasmids and prokaryotes. When a homologous gene is present on at least one plasmid or virus and at least one chromosome, a process of “gene externalization,” affected by a postprocessed selected functional bias, takes place, especially in Bacteria. Bipartite graphs give us a view of vertical and horizontal gene flow beyond classic taxonomy on a single very large, analytically tractable, graph that goes beyond the cellular Web of Life.

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Section: Resultsmentioning

confidence: 99%

Bipartite Network Analysis of Gene Sharings in the Microbial World

Corel

Méheust

Watson

et al. 2018

Molecular Biology and Evolution

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“…The primers, cycling conditions and qPCR methods used to determine cbb gene abundance and transcription level were those reported by Wang et al. 11 …”

Section: Methodsmentioning

confidence: 99%

“… 5 , 6 , 7 , 8 However, the large-scale industrial use of chemoautotrophic bacteria to fix CO 2 is currently limited by their low growth rates and poor ability to fix carbon. 9 , 10 , 11 …”

Section: Introductionmentioning

confidence: 99%

“…In contrast to previous research, which mainly focused on the external factors that inhibit bacterial CO 2 fixation, 11 , 19 , 20 in this study, we investigated the components of self-generated EFOC that inhibit CO 2 fixation by chemoautotrophic bacteria and their mechanisms. Our results provide a theoretical basis for developing targeted measures to remove the main inhibitory components from cultures of chemoautotrophic bacteria to improve their CO 2 fixation, such as the affinity adsorption of small-molecule EFOC, and circulating flow technology with microfiltration membranes for large-molecule EFOC.…”

Section: Introductionmentioning

confidence: 99%

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Main components of free organic carbon generated by obligate chemoautotrophic bacteria that inhibit their CO2 fixation

Zhang

Han

et al. 2022

iScience

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“…cbbM is the gene that encodes for the form II of the carboxylating enzyme RuBisCO, and previous studies have shown that cbbM gene expression is correlated with carbon fixation efficiency and yield 47,48 . ATP citrate lyase (aclAB) is one of four key enzymes needed to run the TCA cycle in reverse (the other three being fumarate reductase, 2-oxoglutarate ferredoxin oxidoreductase (OGOR) and pyruvate ferredoxin oxidoreductase (PFOR)).…”

Section: Differential Expression Of Key Genes Involved In the Cbb And...mentioning

confidence: 99%

Beyond the single pathway: co-expression analysis reveals distinct roles of dual carbon fixation in Riftia pachyptila symbionts

Girguis

Mitchell

Freedman

et al. 2023

Preprint

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Biological carbon fixation is foundational to the biosphere. Most organisms possess one carbon fixation pathway. The hydrothermal vent tubeworm Riftia pachyptila’s chemoautotrophic symbionts, however, possess two functional pathways: the Calvin Benson-Bassham (CBB) and the reductive tricarboxylic acid (rTCA) cycles. Little is known about how Riftia’s symbionts and related organisms coordinate the functioning of these two pathways. Here we investigated net carbon fixation rates, transcriptional/metabolic responses, and transcriptional co-expression patterns of Riftia pachyptila’s endosymbionts by incubating tubeworms at environmental pressures, temperature, and geochemistry. Results showed that rTCA and CBB transcriptional patterns varied in response to different geochemical regimes and that each pathway is allied to specific metabolic processes, suggesting distinctive yet complementary roles in metabolic function. Net carbon fixation rates were also exemplary, and accordingly we propose that co-activity of CBB and rTCA may be an adaptation for maintaining high carbon fixation rates, conferring a fitness advantage in dynamic vent environments.

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Response of cbb gene transcription levels of four typical sulfur-oxidizing bacteria to the CO 2 concentration and its effect on their carbon fixation efficiency during sulfur oxidation

Cited by 19 publications

References 38 publications

Bipartite Network Analysis of Gene Sharings in the Microbial World

Bipartite Network Analysis of Gene Sharings in the Microbial World

Main components of free organic carbon generated by obligate chemoautotrophic bacteria that inhibit their CO2 fixation

Beyond the single pathway: co-expression analysis reveals distinct roles of dual carbon fixation in Riftia pachyptila symbionts

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