Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea

Author(s)

Gomes-Filho, Jose Vicente ^[1] ; Zaramela, Livia Soares ^[1] ; da Silva Italiani, Valeria Cristina ^[1] ; Baliga, Nitin S. ^[2] ; Vencio, Ricardo Z. N. ^[3] ; Koide, Tie ^[1]

Affiliation

^[1] Univ Sao Paulo, Ribeirao Preto Med Sch, Dept Biochem & Immunol, BR-14049 Ribeirao Preto - Brazil

^[2] Inst Syst Biol, Seattle, WA - USA

^[3] Univ Sao Paulo, Dept Comp & Math, Fac Filosofia Ciencias & Letras Ribeirao Preto, BR-14049 Ribeirao Preto - Brazil

• Document type: Journal article
• Source: RNA BIOLOGY; v. 12, n. 5, p. 490-500, MAY 4 2015.
• Web of Science Citations: 7

Abstract

The existence of sense overlapping transcripts that share regulatory and coding information in the same genomic sequence shows an additional level of prokaryotic gene expression complexity. Here we report the discovery of ncRNAs associated with IS1341-type transposase (tnpB) genes, at the 3'-end of such elements, with examples in archaea and bacteria. Focusing on the model haloarchaeon Halobacterium salinarum NRC-1, we show the existence of sense overlapping transcripts (sotRNAs) for all its IS1341-type transposases. Publicly available transcriptome compendium show condition-dependent differential regulation between sotRNAs and their cognate genes. These sotRNAs allowed us to find a UUCA tetraloop motif that is present in other archaea (ncRNA family HgcC) and in a H. salinarum intergenic ncRNA derived from a palindrome associated transposable elements (PATE). Overexpression of one sotRNA and the PATE-derived RNA harboring the tetraloop motif improved H. salinarum growth, indicating that these ncRNAs are functional. (AU)

• FAPESP's process: 13/21522-5 - Functional characterization of non-coding RNAs associated with IS1341 transposons in Halobacterium salinarum
• Grantee: José Vicente Gomes Filho
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 10/10195-5 - Characterization of the non-coding RNAs in the extremophile Halobacterium salinarum
• Grantee: Valéria Cristina da Silva Italiani
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 11/07487-7 - Identification and characterization of Lsm-binding non-coding RNAs in the extremophile Halobacterium salinarum
• Grantee: Lívia Soares Zaramela
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 09/09532-0 - Systems biology of the extremophile Halobacterium salinarum: role of the non-coding RNAs in the global gene regulatory network model
• Grantee: Tie Koide
• Support Opportunities: Research Grants - Young Investigators Grants