Complete genome sequence of Aquitalea pelogenes USM4 (JCM19919), a polyhydroxyalkanoate producer

Wan, Jia Hui; Ng, Lee-Mei; Neoh, Soon Zher; Kajitani, Rei; Itoh, Takehiko; Kajiwara, Susumu; Sudesh, Kumar

doi:10.1007/s00203-023-03406-1

Cited by 4 publications

(4 citation statements)

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“…To date, the most common strategy for the formation of a single granule in the bacterial cell is by deletion of phaP s [ 26 , 65 , 66 ]. Previously, a similar observation was obtained through N-and C-terminal truncation of PhaC Ap [ 36 , 50 ]. But the stark difference in the PHA granule morphology was that even the full-length PhaC BP-M-CPF4 accumulated lesser PHA granules compared to the full-length PhaC Ap .…”

Section: Discussionsupporting

confidence: 72%

“…This study successfully engineered PhaC with the desired properties by truncating the N-terminal region of PhaC BP-M-CPF4 . In a previous study by Lim and co-workers, N-terminal truncation of PhaC from Aquitalea pelogenes USM4 (PhaC Ap ) resulted in a significant decrease in the number of PHA granules as well [ 36 , 50 ]. This observation provided an impetus to this study whereby a more versatile PhaC discovered from mangrove soil metagenome was subjected to further improvement.…”

Section: Discussionmentioning

confidence: 99%

“…But the stark difference in the PHA granule morphology was that even the full-length PhaC BP-M-CPF4 accumulated lesser PHA granules compared to the full-length PhaC Ap . To date, there was still no knowledge regarding the origin of this PhaC BP-M-CPF4 which was isolated from mangrove soil metagenome, unlike PhaC Ap where we know that it comes from A. pelogenes USM4 [ 8 , 50 ].…”

Section: Discussionmentioning

confidence: 99%

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N-terminal truncation of PhaCBP-M-CPF4 and its effect on PHA production

Neoh,

Tan,

Trakunjae

et al. 2024

Microb Cell Fact

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Background Among the polyhydroxyalkanoate (PHA), poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)] is reported to closely resemble polypropylene and low-density polyethylene. Studies have shown that PHA synthase (PhaC) from mangrove soil (PhaCBP-M-CPF4) is an efficient PhaC for P(3HB-co-3HHx) production and N-termini of PhaCs influence its substrate specificity, dimerization, granule morphology, and molecular weights of PHA produced. This study aims to further improve PhaCBP-M-CPF4 through N-terminal truncation. Results The N-terminal truncated mutants of PhaCBP-M-CPF4 were constructed based on the information of the predicted secondary and tertiary structures using PSIPRED server and AlphaFold2 program, respectively. The N-terminal truncated PhaCBP-M-CPF4 mutants were evaluated in C. necator mutant PHB−4 based on the cell dry weight, PHA content, 3HHx molar composition, molecular weights, and granule morphology of the PHA granules. The results showed that most transformants harbouring the N-terminal truncated PhaCBP-M-CPF4 showed a reduction in PHA content and cell dry weight except for PhaCBP-M-CPF4 G8. PhaCBP-M-CPF4 G8 and A27 showed an improved weight-average molecular weight (Mw) of PHA produced due to lower expression of the truncated PhaCBP-M-CPF4. Transformants harbouring PhaCBP-M-CPF4 G8, A27, and T74 showed a reduction in the number of granules. PhaCBP-M-CPF4 G8 produced higher Mw PHA in mostly single larger PHA granules with comparable production as the full-length PhaCBP-M-CPF4. Conclusion This research showed that N-terminal truncation had effects on PHA accumulation, substrate specificity, Mw, and granule morphology. This study also showed that N-terminal truncation of the amino acids that did not adopt any secondary structure can be an alternative to improve PhaCs for the production of PHA with higher Mw in mostly single larger granules.

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Section: Discussionsupporting

confidence: 72%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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N-terminal truncation of PhaCBP-M-CPF4 and its effect on PHA production

Neoh,

Tan,

Trakunjae

et al. 2024

Microb Cell Fact

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“…Despite these general benefits, however, all current state-of-the-art hybrid assembly approaches that can be applied for metagenomes (31; 32; 33; 34) operate at the species level, as the finest taxonomic resolution. Note that all of them have been widely applied in studies that require metagenomic assembly as an essential step (35; 36; 37; 38; 39).…”

Section: Introductionmentioning

confidence: 99%

HyLight: Strain aware assembly of low coverage metagenomes

Kang,

Zhang,

Luo

et al. 2023

Preprint

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Different strains of identical species can vary substantially in terms of their spectrum of biomedically relevant phenotypes. Reconstructing the genomes of a microbial community at strain level poses major methodical challenges, because relative frequencies of individual strains match the rate of sequencing errors, which hampers the identification of their characteristic genetic variants. While next-generation sequencing (NGS) reads are too short to span complex repetitive regions, the considerably longer third-generation sequencing (TGS) reads are affected by larger sequencing error rates or are just significantly more expensive. Suppressing TGS coverage to limit costs implies losses in terms of the accuracy of the assemblies. Therefore, existing approaches have remained fragmentary: all approaches presented so far agree on losses in strain awareness, accuracy, possibly excessive costs of the assemblies, or combinations thereof.We present HyLight as, to the best of our knowledge, the first metagenome assembly approach that is not affected by any of the aforementioned drawbacks. In experiments, we demonstrate that HyLight assemblies are strain-aware, contiguous, contain little errors, and because operating on low coverage TGS data of the cheap kind, come at drastically reduced costs. HyLight implements hybrid assembly, which exploits the complementarity of TGS and NGS data. For unifying the two types of data, HyLight utilizes strain resolved overlap graphs (OG), which support the accurate reconstruction of the individual members of microbial communities at strain level: HyLight outperforms existing approaches in terms of strain identity preserving sequence by on average 25.53% (across all experiments / data sets: first quartile: 21.53%, median: 26.81%, third quartile: 31.98%), achieving near-complete strain awareness on many data sets. In summary, HyLight appears to implement the first protocol that delivers assemblies that are strain-aware, contiguous and accurate in combination.

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HyLight: Strain aware assembly of low coverage metagenomes

Kang,

Zhang,

et al. 2024

Nat Commun

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Different strains of identical species can vary substantially in terms of their spectrum of biomedically relevant phenotypes. Reconstructing the genomes of microbial communities at the level of their strains poses significant challenges, because sequencing errors can obscure strain-specific variants. Next-generation sequencing (NGS) reads are too short to resolve complex genomic regions. Third-generation sequencing (TGS) reads, although longer, are prone to higher error rates or substantially more expensive. Limiting TGS coverage to reduce costs compromises the accuracy of the assemblies. This explains why prior approaches agree on losses in strain awareness, accuracy, tendentially excessive costs, or combinations thereof. We introduce HyLight, a metagenome assembly approach that addresses these challenges by implementing the complementary strengths of TGS and NGS data. HyLight employs strain-resolved overlap graphs (OG) to accurately reconstruct individual strains within microbial communities. Our experiments demonstrate that HyLight produces strain-aware and contiguous assemblies at minimal error content, while significantly reducing costs because utilizing low-coverage TGS data. HyLight achieves an average improvement of 19.05% in preserving strain identity and demonstrates near-complete strain awareness across diverse datasets. In summary, HyLight offers considerable advances in metagenome assembly, insofar as it delivers significantly enhanced strain awareness, contiguity, and accuracy without the typical compromises observed in existing approaches.

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Complete genome sequence of Aquitalea pelogenes USM4 (JCM19919), a polyhydroxyalkanoate producer

Cited by 4 publications

References 66 publications

N-terminal truncation of PhaCBP-M-CPF4 and its effect on PHA production

N-terminal truncation of PhaCBP-M-CPF4 and its effect on PHA production

HyLight: Strain aware assembly of low coverage metagenomes

HyLight: Strain aware assembly of low coverage metagenomes

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