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BMC Genomics. 2016 Feb 29;17:154. doi: 10.1186/s12864-016-2474-z.

Functional elucidation of the non-coding RNAs of Kluyveromyces marxianus in the exponential growth phase.

Author information

1
Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Republic of Korea. newman73@gmail.com.
2
Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Republic of Korea. lej7510@kaist.ac.kr.
3
Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Republic of Korea. shcho95@gmail.com.
4
Biomaterials Lab., Samsung Advanced Institute of Technology (SAIT), 130 Samsung-ro, Yeongtong-gu, Suwon, 443-803, Republic of Korea. ty76.kim@samsung.com.
5
Biomaterials Lab., Samsung Advanced Institute of Technology (SAIT), 130 Samsung-ro, Yeongtong-gu, Suwon, 443-803, Republic of Korea. jh111.park@samsung.com.
6
Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Republic of Korea. bcho@kaist.ac.kr.
7
Intelligent Synthetic Biology Center, Daejeon, 305-701, Republic of Korea. bcho@kaist.ac.kr.

Abstract

BACKGROUND:

Non-coding RNAs (ncRNAs), which perform diverse regulatory roles, have been found in organisms from all superkingdoms of life. However, there have been limited numbers of studies on the functions of ncRNAs, especially in nonmodel organisms such as Kluyveromyces marxianus that is widely used in the field of industrial biotechnology.

RESULTS:

In this study, we measured changes in transcriptome at three time points during the exponential growth phase of K. marxianus by using strand-specific RNA-seq. We found that approximately 60% of the transcriptome consists of ncRNAs transcribed from antisense and intergenic regions of the genome that were transcribed at lower levels than mRNA. In the transcriptome, a substantial number of long antisense ncRNAs (lancRNAs) are differentially expressed and enriched in carbohydrate and energy metabolism pathways. Furthermore, this enrichment is evolutionarily conserved, at least in yeast. Particularly, the mode of regulation of mRNA/lancRNA pairs is associated with mRNA transcription levels; the correlation between the pairs is positive at high mRNA transcriptional levels and negative at low levels. In addition, significant induction of mRNA and coverage of more than half of the mRNA sequence by a lancRNA strengthens the positive correlation between mRNA/lancRNA pairs.

CONCLUSIONS:

Transcriptome sequencing of K. marxianus in the exponential growth phase reveals pervasive transcription of ncRNAs with evolutionarily conserved functions. Studies of the mode of regulation of mRNA/lancRNA pairs suggest that induction of lancRNA may be associated with switch-like behavior of mRNA/lancRNA pairs and efficient regulation of the carbohydrate and energy metabolism pathways in the exponential growth phase of K. marxianus being used in industrial applications.

PMID:
26923790
PMCID:
PMC4770515
DOI:
10.1186/s12864-016-2474-z
[Indexed for MEDLINE]
Free PMC Article

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