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Functional characterization and high-throughput proteomic analysis of interrupted genes in the archaeon Sulfolobus solfataricus (Articolo in rivista)

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Functional characterization and high-throughput proteomic analysis of interrupted genes in the archaeon Sulfolobus solfataricus (Articolo in rivista) (literal)

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Cobucci-Ponzano B.; Guzzini L.; Benelli D.; Londei P.; Perrodou E.; Lecompte O.; Tran D.; Sun J.; Wei J.; Mathur E.J.; Rossi M.; Moracci M. (2010)
Functional characterization and high-throughput proteomic analysis of interrupted genes in the archaeon Sulfolobus solfataricus
in Journal of proteome research (Print); American Chemical Society, Washington (Stati Uniti d'America)
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Cobucci-Ponzano B.; Guzzini L.; Benelli D.; Londei P.; Perrodou E.; Lecompte O.; Tran D.; Sun J.; Wei J.; Mathur E.J.; Rossi M.; Moracci M. (literal)

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Institute of Protein Biochemistry-CNR, Via P. Castellino 111, 80131 Naples, Italy Dipartimento di Biotecnologie Cellulari ed Ematologia, Universita` di Roma Sapienza, Policlinico Umberto I, Viale Regina Elena 324, 00161 Roma, Italy Department of Structural Biology and Genomics, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), F-67400 Illkirch, France AviaraDx, Inc., 11025 Roselle Street, Suite 200, San Diego, California 92121, Genomatica, Inc., 10520 Wateridge Circle, San Diego, California 92121 BiogenIdec Corporation, 5200 Research Place, San Diego, California 92121 Synthetic Genomics, Inc., 11149 North Torrey Pines Road, La Jolla, California 92037 Dipartimento di Biologia Strutturale e Funzionale, Universita` di Napoli \"Federico II\", Complesso Universitario di Monte S. Angelo, Via Cinthia 4, 80126 Naples, Italy (literal)

Titolo

Functional characterization and high-throughput proteomic analysis of interrupted genes in the archaeon Sulfolobus solfataricus (literal)

Abstract

Sequenced genomes often reveal interrupted coding sequences that complicate the annotation process and the subsequent functional characterization of the genes. In the past, interrupted genes were generally considered to be the result of sequencing errors or pseudogenes, i.e. gene remnants with little or no biological importance. However, recent lines of evidence support the hypothesis that these coding sequences can be functional, thus, it is crucial to understand whether interrupted genes are expressed in vivo. We addressed this issue by experimentally demonstrating the existence of functional disrupted genes in archaeal genomes. We discovered previously unknown disrupted genes that have interrupted homologues in distantly related species of archaea. The combination of a RT-PCR strategy with shotgun proteomics demonstrates that interrupted genes in the archaeon Sulfolobus solfataricus are expressed in vivo. In addition, the sequence of the peptides determined by LCMSMS and experiments of in vitro translation allows us to identify a gene expressed by programmed -1 frameshifting. Our findings will enable an accurate re-interpretation of archaeal interrupted genes shedding light on their function and on archaeal genome evolution. (literal)

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