Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs

Zhu, Yunchi; Lü, Na; Chen, Jy; He, Chunpeng; He, Chunpeng; Zhang, Lu

doi:10.1186/s12863-022-01038-w

Cited by 5 publications

(4 citation statements)

References 57 publications

(46 reference statements)

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“…It has been demonstrated that amphioxus is one of the most genetically diverse animals sequenced to date 49 – 51 . Somatic mutation frequency per nucleotide in amphioxus (10 −3 ) 52 is orders of magnitude higher than in other multicellular eukaryotes, including mammals (10 −7 ) 53 , 54 , fly (10 −5 ) 55 and coral (10 −7 ) 56 , while mutational processes in amphioxus are unknown.…”

Section: Discussionmentioning

confidence: 99%

Amphioxus adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U and A-to-I deamination of DNA

et al. 2023

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Adenosine-to-inosine tRNA-editing enzyme has been identified for more than two decades, but the study on its DNA editing activity is rather scarce. We show that amphioxus (Branchiostoma japonicum) ADAT2 (BjADAT2) contains the active site ‘HxE-PCxxC’ and the key residues for target-base-binding, and amphioxus ADAT3 (BjADAT3) harbors both the N-terminal positively charged region and the C-terminal pseudo-catalytic domain important for recognition of substrates. The sequencing of BjADAT2-transformed Escherichia coli genome suggests that BjADAT2 has the potential to target E. coli DNA and can deaminate at TCG and GAA sites in the E. coli genome. Biochemical analyses further demonstrate that BjADAT2, in complex with BjADAT3, can perform A-to-I editing of tRNA and convert C-to-U and A-to-I deamination of DNA. We also show that BjADAT2 preferentially deaminates adenosines and cytidines in the loop of DNA hairpin structures of substrates, and BjADAT3 also affects the type of DNA substrate targeted by BjADAT2. Finally, we find that C89, N113, C148 and Y156 play critical roles in the DNA editing activity of BjADAT2. Collectively, our study indicates that BjADAT2/3 is the sole naturally occurring deaminase with both tRNA and DNA editing capacity identified so far in Metazoa.

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Section: Discussionmentioning

confidence: 99%

Amphioxus adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U and A-to-I deamination of DNA

et al. 2023

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“…Compared to other prediction algorithms such as RoseTTAFold [ 18 ], AlphaFold2 has obvious disadvantages in performance [ 19 ], as even protein domains can consume long computation times [ 20 ]. Fortunately, its open source has attracted joint efforts of developers to improve it.…”

Section: Introductionmentioning

confidence: 99%

Utilizing an artificial intelligence system to build the digital structural proteome of reef-building corals

et al. 2022

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Background Reef-building corals play an important role in the marine ecosystem, and analyzing their proteomes from a structural perspective will exert positive effects on exploring their biology. Here we integrated mass spectrometry with newly published ColabFold to obtain digital structural proteomes of dominant reef-building corals. Results Of the 8,382 homologous proteins in Acropora muricata, Montipora foliosa, and Pocillopora verrucosa identified, 8,166 received predicted structures after about 4,060 GPU hours of computation. The resulting dataset covers 83.6% of residues with a confident prediction, while 25.9% have very high confidence. Conclusions Our work provides insight-worthy predictions for coral research, confirms the reliability of ColabFold in practice, and is expected to be a reference case in the impending high-throughput era of structural proteomics.

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“…Compared to other prediction algorithms such as RoseTTAFold [18], AlphaFold2 has obvious disadvantages in performance, even domains could consume long computation time [19].…”

Section: Introductionmentioning

confidence: 99%

“…Compared to other prediction algorithms such as RoseTTAFold [18], AlphaFold2 has obvious disadvantages in performance, even domains could consume long computation time [19]. Fortunately, its open source has attracted joint efforts of developers to improve it.…”

Section: Introductionmentioning

confidence: 99%

Utilizing artificial intelligence system to build the digital structural proteome of reef-building corals

Zhu

Liao

Han

et al. 2022

Preprint

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Reef-building corals play an important role in the marine ecosystem, and analyzing their proteomes from a structural perspective will exert positive effects on exploring their biology. Here we integrated mass spectrometry with newly published ColabFold to obtain digital structural proteomes of dominant reef-building corals. 8,382 proteins co-expressed in A. muricata, M. foliosa and P. verrucosa were identified, then 8,166 of them got predicted structures after around 4,060 GPU hours of computation. The resulting dataset covers 83.6% of residues with a confident prediction, while 25.9% have very high confidence. Our work provides insight-worthy predictions for coral research, confirms the reliability of ColabFold in practice, and is expected to be a reference case in the impending high-throughput era of structural proteomics.

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Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs

Cited by 5 publications

References 57 publications

Amphioxus adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U and A-to-I deamination of DNA

Amphioxus adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U and A-to-I deamination of DNA

Utilizing an artificial intelligence system to build the digital structural proteome of reef-building corals

Utilizing artificial intelligence system to build the digital structural proteome of reef-building corals

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