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Muthu, G.

Publications and source records attributed to Muthu, G..

3 recordsLinked to original sources

A conserved Pho4-Pho84 axis ubiquitously maintains intracellular phosphate homeostasis in yeast

Inorganic phosphate (Pi) is central to fundamental cellular processes and the metabolic economy, and is constantly acquired in order to maintain intracellular Pi levels. While much is known about cellular adaptation during Pi starvation, how intracellular Pi is maintained in Pi-replete conditions remains unclear. Here, using Saccharomyces cerevisiae, we uncover an essential role for the Pho4 transcription factor in maintaining intracellular Pi under Pi-replete conditions, via the high affinity Pho84 transporter. Basal Pho4-dependent output is required for intracellular Pi maintenance, and the loss of Pho4 results in decreased intracellular Pi. We uncover that the Pho4 dependent, high affinity Pi transporter Pho84 is the primary transporter required for this intracellular Pi maintenance in phosphate replete conditions, and is not compensated by other transporters. The loss of Pho4 or Pho84 decreases intracellular Pi, with reduced ATP and glycolysis, and decreased growth. Through comparative genomic and phylogenetic analyses we establish that Pho84 is universally conserved across fungi, and Pho84 alone is orthologous to the plant high-affinity phosphate transporter PHT1. Thus, Pho84 is a primary determinant of intracellular Pi homeostasis during phosphate replete growth, and Pi acquisition in replete conditions is built around high-affinity phosphate transport. These findings reiterate the importance of Pi acquisition via high-affinity transport for metabolic homeostasis, with implications for microbial fermentation-based applications.

systems biology↗

Evolutionary analysis of Trehalose breakdown pathways

Trehalose is a widely prevalent, abundant disaccharide that acts as a cellular stress protectant, and functions as an energy source that enters central carbon metabolism when broken down. The evolution and distribution of trehalose breakdown pathways across kingdoms of life have not been studied, and therefore the ability of different organisms to consume trehalose as a carbon source is unknown. In this study, we build a comprehensive evolutionary analysis of the four known trehalose breakdown pathways - trehalase (acid, neutral, glycosyl hydrolase 15), trehalose phosphorylases (TP, treP), and trehalose specific phosphotransferases (PTS), by studying their distributions across ~4000 prokaryotic and eukaryotic genomes. Our study suggests the presence of trehalase in the Last Eukaryotic Common Ancestor (LECA), and reveals near-universal presence of trehalase in eukaryotes, except in all birds where trehalase was lost in the first bird ancestor. Fungi alone retain additional trehalose phosphorylases (TP) in addition to trehalase. In contrast, trehalose breakdown in prokaryotes is highly sporadic but can occur via multiple, independently evolved pathways, including trehalase, the trehalose-specific PTS and trehalose phosphorylase. Finally, we observe that a subset of fast-growing Gammaproteobacteria retain the trehalose specific PTS, the loss of which reduces growth in Escherichia coli. Overall, our findings uncover the evolutionary landscape of trehalose breakdown, and use of this versatile disaccharide as an energy reserve in different kingdoms of life.

genomics↗

Evolution of transcription factor-containing superfamilies in Eukaryotes

Regulation of gene expression helps determine various phenotypes in most cellular life forms. It is orchestrated at different levels and at the point of transcription initiation by transcription factors (TFs). TFs bind to DNA through domains that are evolutionarily related, by shared membership of the same superfamilies (TF-SFs), to those found in other nucleic acid binding and protein-binding functions (nTFs for non-TFs). Here we ask how TF DNA binding sequence families in eukaryotes have evolved in relation to their nTF relatives. TF numbers scale by power law with the total number of protein-coding genes differently in different clades, with fungi usually showing sub-linear powers whereas chordates show super-linear scaling. The LECA probably encoded a complex regulatory machinery with both TFs and nTFs, but with an excess of nTFs when compared to the relative distribution of TFs and nTFs in extant organisms. Losses drive the evolution of TFs and nTFs, with the possible exception of TFs in Animalia for some tree topologies. TFs are highly dynamic in evolution, showing higher gain and loss rates than nTFs though both are conserved to similar extents. Gains of TFs and nTFs are driven by the appearance of a large number of new sequence clusters in a small number of nodes, which determine the presence of as many as a third of extant TFs and nTFs as well as the relative presence of TFs and nTFs. Whereas nodes showing explosion of TF numbers belong to multicellular clades, those for nTFs lie among the fungi and the protists.

genomics↗