Archive for category My Publications

Recent Advances in the Molecular Study of Circadian Clocks in Neurospora and Other Fungi

Together with Paulo Canessa and Luis Larrondo, we wrote an extensive review on circadian rhythms in fungi, which was published in Advances in Genetics. We focused on the well-characterized clock of the ascomycete Neurospora crassa, describing the molecular basis of its pacemaker, together with how it synchronizes with the environment and how it controls the rhythmic expression of thousands of genes. We mostly centered our discussion on recent research on all of these topics. We also described several studies reporting rhythms in other fungi and towards the end of the article, we focused on the clock of the pathogenic fungus Botrytis cinerea, for which we have recently described a functional circadian clock that plays a major role in determining the outcome of the Arabidopsis-Botrytis interaction.

Here’s the info:

Around the Fungal Clock: Recent Advances in the Molecular Study of Circadian Clocks in Neurospora and Other Fungi

Advances in Genetics
Available online 27 October 2015
In Press, Corrected Proof

Alejandro Montenegro-Montero, Paulo Canessa, Luis F. Larrondo

N. crassa growing on solid media under light-dark conditions

N. crassa growing on solid media under light-dark conditions

Abstract
Night follows day and as a consequence, organisms have evolved molecular machineries that allow them to anticipate and respond to the many changes that accompany these transitions. Circadian clocks are precise yet plastic pacemakers that allow the temporal organization of a plethora of biological process. Circadian clocks are widespread across the tree of life and while their exact molecular components differ among phyla, they tend to share common design principles. In this review, we discuss the circadian system of the filamentous fungus Neurospora crassa. Historically, this fungus has served a key role in the genetic and molecular dissection of circadian clocks, aiding in their detailed mechanistic understanding. Recent studies have provided new insights into the daily molecular dynamics that constitute the Neurospora circadian oscillator, some of which have questioned traditional paradigms describing timekeeping mechanisms in eukaryotes. In addition, recent reports support the idea of a dynamic network of transcription factors underlying the rhythmicity of thousands of genes in Neurospora, many of which oscillate only under specific conditions. Besides Neurospora, which harbors the best characterized circadian system among filamentous fungi, the recent characterization of the circadian system of the plant-pathogenic fungus Botrytis cinerea has provided additional insights into the physiological impact of the clock and potential additional functions of clock proteins in fungi. Finally, we speculate on the presence of FRQ or FRQ-like proteins in diverse fungal lineages.

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The Case for Transcriptional Regulation and Coupling as Relevant Determinants of the Circadian Transcriptome and Proteome in Eukaryotes

My latest paper is out, a commentary, in which together with Luis Larrondo, we evaluate evidence regarding the relative contribution of the different steps of gene expression (transcriptional, post-transcriptional, translational, etc.) in determining daily mRNA and protein rhythms in eukaryotes. We argue that it’s too early to assign a predominant role for one specific stage in this process, as some papers have done, due to a variety of biological and particularly, technical, reasons. We further propose that RNAPII recruitment is rhythmic on a global scale, setting the stage for global nascent transcription, but that tissue-specific mechanisms ultimately locally specify the different processes under clock control.

Here’s the link and info:

In the Driver’s Seat: The Case for Transcriptional Regulation and Coupling as Relevant Determinants of the Circadian Transcriptome and Proteome in Eukaryotes

Published online before print October 7, 2015, doi: 10.1177/0748730415607321
J Biol Rhythms October 7, 2015 0748730415607321

Abstract

Circadian clocks drive daily oscillations in a variety of biological processes through the coordinate orchestration of precise gene expression programs. Global expression profiling experiments have suggested that a significant fraction of the transcriptome and proteome is under circadian control, and such output rhythms have historically been assumed to rely on the rhythmic transcription of these genes. Recent genome-wide studies, however, have challenged this long-held view and pointed to a major contribution of posttranscriptional regulation in driving oscillations at the messenger RNA (mRNA) level, while others have highlighted extensive clock translational regulation, regardless of mRNA rhythms. There are various examples of genes that are uniformly transcribed throughout the day but that exhibit rhythmic mRNA levels, and of flat mRNAs, with oscillating protein levels, and such observations have largely been considered to result from independent regulation at each step. These studies have thereby obviated any connections, or coupling, that might exist between the different steps of gene expression and the impact that any of them could have on subsequent ones. Here, we argue that due to both biological and technical reasons, the jury is still out on the determination of the relative contributions of each of the different stages of gene expression in regulating output molecular rhythms. In addition, we propose that through a variety of coupling mechanisms, gene transcription (even when apparently arrhythmic) might play a much relevant role in determining oscillations in gene expression than currently estimated, regulating rhythms at downstream steps. Furthermore, we posit that eukaryotic genomes regulate daily RNA polymerase II (RNAPII) recruitment and histone modifications genome-wide, setting the stage for global nascent transcription, but that tissue-specific mechanisms locally specify the different processes under clock control.

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