Draft Genome Assembly of Rhodobacter sphaeroides 2.4.1 Substrain H2 from Nanopore Data

Leidenfrost, Robert Maximilian; Wappler, Nadine; Wünschiers, Röbbe

doi:10.1128/mra.00414-20

Cited by 3 publications

(4 citation statements)

References 26 publications

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“… 23 Rhodobacter sphaeroides strain 2.4.1 – – NA NA NA Leidenfrost et al. 25 H9 – – NA NA NA Weaver et al. 24 P12F1 – – NA NA NA Weaver et al.…”

Section: Resultsmentioning

confidence: 99%

Jorvik: A membrane-containing phage that will likely found a new family within Vinavirales

Bárdy,

MacDonald,

Pantůček

et al. 2023

iScience

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“… 23 Rhodobacter sphaeroides strain 2.4.1 – – NA NA NA Leidenfrost et al. 25 H9 – – NA NA NA Weaver et al. 24 P12F1 – – NA NA NA Weaver et al.…”

Section: Resultsmentioning

confidence: 99%

Jorvik: A membrane-containing phage that will likely found a new family within Vinavirales

Bárdy,

MacDonald,

Pantůček

et al. 2023

iScience

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“…We sequenced the genome of a Cereibacter sphaeroides strain 2.4.1 substrain H2 (named C.s. substrain H2 throughout this publication; BioProject ID PRJNA392388) that is a promising candidate for photofermentative hydrogen production from organic waste [25].…”

Section: Genomic Characterizationmentioning

confidence: 99%

“…Here we characterize Cereibacter sphaeroides strain 2.4.1 substrain H2 that produces hydrogen gas in the presence of relatively high substrate organic nitrogen concentrations. Recently, we presented a first draft of its genome structure [25]. Here, we present our results on genomic mutations, probably acquired during lab cultivation, that cause transcriptomic changes which help to explain decoupling of the cellular organic nitrogen status and hydrogen evolution.…”

Section: Introductionmentioning

confidence: 97%

Analysis of a σ54 Transcription Factor L420P Mutation in Context of Increased Organic Nitrogen Tolerance of Photofermentative Hydrogen Production in Cereibacter sphaeroides Strain 2.4.1 Substrain H2

Wappler,

W黱schiers

2024

Synthetic Biology and Engineering

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Photofermentative hydrogen production with non-sulfur purple bacteria like Cereibacter sphaeroides (formerly Rhodobacter sphaeroides) is a promising and sustainable process to convert organic waste into the energy carrier hydrogen gas. However, this conversion is inhibited by elevated organic nitrogen concentrations in the substrate, which limits its applicability to nitrogen-poor organic waste. We present genomic and transcriptomic insights into a substrain of Cereibacter sphaeroides strain 2.4.1 that shows unexpected high levels of photofermentative hydrogen evolution when fed with glutamate. Genome sequencing revealed 222 single nucleotide variances (SNVs) between the reference genome of C. sphaeroides strain 2.4.1 and the analyzed substrain H2. These affect 61 protein coding genes. A leucine-proline exchange is present in the σ 54 factor (rpoN2 gene), a global hydrogen and nitrogen metabolism regulator. We propose a model how this mutation alters DNA-binding properties that explain the unexpected organic nitrogen tolerance of hydrogen production. Transcriptomic analyses under varying glutamate concentrations support this finding. Thus, we present the first thorough genomic and transcriptomic analysis of a Cereibacter strain that shows promising metabolic characteristics for biotechnological hydrogen gas production from organic waste. These results suggest a potential target for strain optimization. Possibly, our key finding can be transferred to other hydrogen producing microorganisms.

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“…Notably, PGAP reports that the number of pseudogenes is about 30% of the gene features (2,432 pseudogenes out of 8,048 coding DNA sequences). These are probably caused by indels, which are typical for nanopore sequencing-only assemblies ( 11 ).…”

Section: Announcementmentioning

confidence: 99%

Whole-genome sequence of Paenibacillus amylolyticus strain W018, isolated from Triticum aestivum L. seeds, obtained using nanopore sequencing

Chebotar,

Gancheva,

Chizhevskaya

et al. 2023

Microbiol Resour Announc

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Draft Genome Assembly of Rhodobacter sphaeroides 2.4.1 Substrain H2 from Nanopore Data

Abstract: Rhodobacter sphaeroides is a purple bacterium with complex genomic architecture. Here, a draft genome is reported for R. sphaeroides strain 2.4.1 substrain H2, which was generated exclusively from Nanopore sequencing data.

Cited by 3 publications

References 26 publications

Jorvik: A membrane-containing phage that will likely found a new family within Vinavirales

Jorvik: A membrane-containing phage that will likely found a new family within Vinavirales

Analysis of a σ54 Transcription Factor L420P Mutation in Context of Increased Organic Nitrogen Tolerance of Photofermentative Hydrogen Production in Cereibacter sphaeroides Strain 2.4.1 Substrain H2

Whole-genome sequence of Paenibacillus amylolyticus strain W018, isolated from Triticum aestivum L. seeds, obtained using nanopore sequencing

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