Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii

Lila Ghamsari, Santhanam Balaji, Yun Shen, Xinping Yang, Dawit Balcha, Changyu Fan, Tong Hao, Haiyuan Yu, Jason A. Papin, Kourosh Salehi-Ashtiani

Research output: Contribution to journalArticle

Abstract

Background: Recent advances in the field of metabolic engineering have been expedited by the availability of genome sequences and metabolic modelling approaches. The complete sequencing of the C. reinhardtii genome has made this unicellular alga a good candidate for metabolic engineering studies; however, the annotation of the relevant genes has not been validated and the much-needed metabolic ORFeome is currently unavailable. We describe our efforts on the functional annotation of the ORF models released by the Joint Genome Institute (JGI), prediction of their subcellular localizations, and experimental verification of their structural annotation at the genome scale.Results: We assigned enzymatic functions to the translated JGI ORF models of C. reinhardtii by reciprocal BLAST searches of the putative proteome against the UniProt and AraCyc enzyme databases. The best match for each translated ORF was identified and the EC numbers were transferred onto the ORF models. Enzymatic functional assignment was extended to the paralogs of the ORFs by clustering ORFs using BLASTCLUST.In total, we assigned 911 enzymatic functions, including 886 EC numbers, to 1,427 transcripts. We further annotated the enzymatic ORFs by prediction of their subcellular localization. The majority of the ORFs are predicted to be compartmentalized in the cytosol and chloroplast. We verified the structure of the metabolism-related ORF models by reverse transcription-PCR of the functionally annotated ORFs. Following amplification and cloning, we carried out 454FLX and Sanger sequencing of the ORFs. Based on alignment of the 454FLX reads to the ORF predicted sequences, we obtained more than 90% coverage for more than 80% of the ORFs. In total, 1,087 ORF models were verified by 454 and Sanger sequencing methods. We obtained expression evidence for 98% of the metabolic ORFs in the algal cells grown under constant light in the presence of acetate.Conclusions: We functionally annotated approximately 1,400 JGI predicted metabolic ORFs that can facilitate the reconstruction and refinement of a genome-scale metabolic network. The unveiling of the metabolic potential of this organism, along with structural verification of the relevant ORFs, facilitates the selection of metabolic engineering targets with applications in bioenergy and biopharmaceuticals. The ORF clones are a resource for downstream studies.

Original languageEnglish (US)
Article numberS4
JournalBMC Genomics
Volume12
Issue numberSUPPL. 1
DOIs
StatePublished - Jun 15 2011

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Chlamydomonas reinhardtii
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Genome
Metabolic Engineering
Joints
Molecular Sequence Annotation

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

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Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii. / Ghamsari, Lila; Balaji, Santhanam; Shen, Yun; Yang, Xinping; Balcha, Dawit; Fan, Changyu; Hao, Tong; Yu, Haiyuan; Papin, Jason A.; Salehi-Ashtiani, Kourosh.

In: BMC Genomics, Vol. 12, No. SUPPL. 1, S4, 15.06.2011.

Research output: Contribution to journalArticle

Ghamsari, L, Balaji, S, Shen, Y, Yang, X, Balcha, D, Fan, C, Hao, T, Yu, H, Papin, JA & Salehi-Ashtiani, K 2011, 'Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii', BMC Genomics, vol. 12, no. SUPPL. 1, S4. https://doi.org/10.1186/1471-2164-12-S1-S4
Ghamsari, Lila ; Balaji, Santhanam ; Shen, Yun ; Yang, Xinping ; Balcha, Dawit ; Fan, Changyu ; Hao, Tong ; Yu, Haiyuan ; Papin, Jason A. ; Salehi-Ashtiani, Kourosh. / Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii. In: BMC Genomics. 2011 ; Vol. 12, No. SUPPL. 1.
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abstract = "Background: Recent advances in the field of metabolic engineering have been expedited by the availability of genome sequences and metabolic modelling approaches. The complete sequencing of the C. reinhardtii genome has made this unicellular alga a good candidate for metabolic engineering studies; however, the annotation of the relevant genes has not been validated and the much-needed metabolic ORFeome is currently unavailable. We describe our efforts on the functional annotation of the ORF models released by the Joint Genome Institute (JGI), prediction of their subcellular localizations, and experimental verification of their structural annotation at the genome scale.Results: We assigned enzymatic functions to the translated JGI ORF models of C. reinhardtii by reciprocal BLAST searches of the putative proteome against the UniProt and AraCyc enzyme databases. The best match for each translated ORF was identified and the EC numbers were transferred onto the ORF models. Enzymatic functional assignment was extended to the paralogs of the ORFs by clustering ORFs using BLASTCLUST.In total, we assigned 911 enzymatic functions, including 886 EC numbers, to 1,427 transcripts. We further annotated the enzymatic ORFs by prediction of their subcellular localization. The majority of the ORFs are predicted to be compartmentalized in the cytosol and chloroplast. We verified the structure of the metabolism-related ORF models by reverse transcription-PCR of the functionally annotated ORFs. Following amplification and cloning, we carried out 454FLX and Sanger sequencing of the ORFs. Based on alignment of the 454FLX reads to the ORF predicted sequences, we obtained more than 90{\%} coverage for more than 80{\%} of the ORFs. In total, 1,087 ORF models were verified by 454 and Sanger sequencing methods. We obtained expression evidence for 98{\%} of the metabolic ORFs in the algal cells grown under constant light in the presence of acetate.Conclusions: We functionally annotated approximately 1,400 JGI predicted metabolic ORFs that can facilitate the reconstruction and refinement of a genome-scale metabolic network. The unveiling of the metabolic potential of this organism, along with structural verification of the relevant ORFs, facilitates the selection of metabolic engineering targets with applications in bioenergy and biopharmaceuticals. The ORF clones are a resource for downstream studies.",
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AU - Ghamsari, Lila

AU - Balaji, Santhanam

AU - Shen, Yun

AU - Yang, Xinping

AU - Balcha, Dawit

AU - Fan, Changyu

AU - Hao, Tong

AU - Yu, Haiyuan

AU - Papin, Jason A.

AU - Salehi-Ashtiani, Kourosh

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N2 - Background: Recent advances in the field of metabolic engineering have been expedited by the availability of genome sequences and metabolic modelling approaches. The complete sequencing of the C. reinhardtii genome has made this unicellular alga a good candidate for metabolic engineering studies; however, the annotation of the relevant genes has not been validated and the much-needed metabolic ORFeome is currently unavailable. We describe our efforts on the functional annotation of the ORF models released by the Joint Genome Institute (JGI), prediction of their subcellular localizations, and experimental verification of their structural annotation at the genome scale.Results: We assigned enzymatic functions to the translated JGI ORF models of C. reinhardtii by reciprocal BLAST searches of the putative proteome against the UniProt and AraCyc enzyme databases. The best match for each translated ORF was identified and the EC numbers were transferred onto the ORF models. Enzymatic functional assignment was extended to the paralogs of the ORFs by clustering ORFs using BLASTCLUST.In total, we assigned 911 enzymatic functions, including 886 EC numbers, to 1,427 transcripts. We further annotated the enzymatic ORFs by prediction of their subcellular localization. The majority of the ORFs are predicted to be compartmentalized in the cytosol and chloroplast. We verified the structure of the metabolism-related ORF models by reverse transcription-PCR of the functionally annotated ORFs. Following amplification and cloning, we carried out 454FLX and Sanger sequencing of the ORFs. Based on alignment of the 454FLX reads to the ORF predicted sequences, we obtained more than 90% coverage for more than 80% of the ORFs. In total, 1,087 ORF models were verified by 454 and Sanger sequencing methods. We obtained expression evidence for 98% of the metabolic ORFs in the algal cells grown under constant light in the presence of acetate.Conclusions: We functionally annotated approximately 1,400 JGI predicted metabolic ORFs that can facilitate the reconstruction and refinement of a genome-scale metabolic network. The unveiling of the metabolic potential of this organism, along with structural verification of the relevant ORFs, facilitates the selection of metabolic engineering targets with applications in bioenergy and biopharmaceuticals. The ORF clones are a resource for downstream studies.

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