Spatio-temporal dynamics of yeast mitochondrial biogenesis: transcriptional and post-transcriptional mRNA oscillatory modules.
PLoS Comput Biol 2009;
5:e1000409. [PMID:
19521515 PMCID:
PMC2690403 DOI:
10.1371/journal.pcbi.1000409]
[Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Accepted: 05/06/2009] [Indexed: 11/19/2022] Open
Abstract
Examples of metabolic rhythms have recently emerged from studies of budding
yeast. High density microarray analyses have produced a remarkably detailed
picture of cycling gene expression that could be clustered according to
metabolic functions. We developed a model-based approach for the decomposition
of expression to analyze these data and to identify functional modules which,
expressed sequentially and periodically, contribute to the complex and intricate
mitochondrial architecture. This approach revealed that mitochondrial
spatio-temporal modules are expressed during periodic spikes and specific
cellular localizations, which cover the entire oscillatory period. For instance,
assembly factors (32 genes) and translation regulators (47 genes) are expressed
earlier than the components of the amino-acid synthesis pathways (31 genes). In
addition, we could correlate the expression modules identified with particular
post-transcriptional properties. Thus, mRNAs of modules expressed
“early” are mostly translated in the vicinity of
mitochondria under the control of the Puf3p mRNA-binding protein. This last
spatio-temporal module concerns mostly mRNAs coding for basic elements of
mitochondrial construction: assembly and regulatory factors. Prediction that
unknown genes from this module code for important elements of mitochondrial
biogenesis is supported by experimental evidence. More generally, these
observations underscore the importance of post-transcriptional processes in
mitochondrial biogenesis, highlighting close connections between nuclear
transcription and cytoplasmic site-specific translation.
In bacterial and eukaryotic cells, gene expression is regulated at both the
transcriptional and translational levels. In eukaryotes these two processes
cannot be directly coupled because the nuclear membrane separates the
chromosomes from the ribosomes. Although the transcription levels in different
cellular conditions have been widely examined, genome-wide post-transcriptional
mechanisms are poorly documented and therefore, the connections between the two
processes are difficult to explain. In this work, the time-regulated expression
of the genes involved in the construction of the mitochondrion, an important
organelle present in nearly all the eukaryotic cells, was scrutinized both at
transcriptional and post-transcriptional levels. We observed that temporal
transcriptional profiles coincide with groups of genes which are translated at
specific cellular loci. The description of these relationships is functionally
relevant since the genes which are transcribed early in mitochondria cycles are
those which are translated to the vicinity of mitochondria. In addition, these
early genes code for essential assembling factors or core elements of the
protein complexes whereas the peripheral proteins are translated later in the
cytoplasm. Also, these observations support the concerted action of important
regulatory factors which control either the gene transcription level
(transcription factors) or the mRNA localization (mRNA-binding proteins).
Collapse