Seripauperins of Saccharomyces cerevisiae: a new multigene family encoding serine-poor relatives of serine-rich proteins

Viswanathan, Manickam; Muthukumar, Ganapathy; Cong, Yu-Sheng; Lenard, John

doi:10.1016/0378-1119(94)90249-6

Cited by 56 publications

(40 citation statements)

References 8 publications

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“…The high transcription of enzymes involved in highly active pathways during fermentation (and possibly not during aerobic respiration) correlates particularly well with the high CAI value of these enzymes. This observation is supported also by the available transcriptomic data on seripauperine proteins (Holstege et al 1998;James et al 2003;Viswanathan et al 1994) and on Hem13 proteins (Amillet et al 1995).…”

Section: Introductionsupporting

confidence: 66%

Insights on the Evolution of Metabolic Networks of Unicellular Translationally Biased Organisms from Transcriptomic Data and Sequence Analysis

Carbone

Madden

2005

J Mol Evol

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Abstract. Codon bias is related to metabolic functions in translationally biased organisms, and two facts are argued about. First, genes with high codon bias describe in meaningful ways the metabolic characteristics of the organism; important metabolic pathways corresponding to crucial characteristics of the lifestyle of an organism, such as photosynthesis, nitrification, anaerobic versus aerobic respiration, sulfate reduction, methanogenesis, and others, happen to involve especially biased genes. Second, gene transcriptional levels of sets of experiments representing a significant variation of biological conditions strikingly confirm, in the case of Saccharomyces cerevisiae, that metabolic preferences are detectable by purely statistical analysis: the high metabolic activity of yeast during fermentation is encoded in the high bias of enzymes involved in the associated pathways, suggesting that this genome was affected by a strong evolutionary pressure that favored a predominantly fermentative metabolism of yeast in the wild. The ensemble of metabolic pathways involving enzymes with high codon bias is rather well defined and remains consistent across many species, even those that have not been considered as translationally biased, such as Helicobacter pylori, for instance, reveal some weak form of translational bias for this genome. We provide numerical evidence, supported by experimental data, of these facts and conclude that the metabolic networks of translationally biased genomes, observable today as projections of eons of evolutionary pressure, can be analyzed numerically and predictions of the role of specific pathways during evolution can be derived. The new concepts of Comparative Pathway Index, used to compare organisms with respect to their metabolic networks, and Evolutionary Pathway Index, used to detect evolutionarily meaningful bias in the genetic code from transcriptional data, are introduced.

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Section: Introductionsupporting

confidence: 66%

Insights on the Evolution of Metabolic Networks of Unicellular Translationally Biased Organisms from Transcriptomic Data and Sequence Analysis

Carbone

Madden

2005

J Mol Evol

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“…Proteins in the latter category have common features, including a region rich in serine and threonine, a glycosylphosphatidylinositol (GPI) anchor attachment signal at C termini (3,8), and an endoplasmic reticulum localization sequence; several also have a PAU domain. This segment of about 100 amino acids is shared among a group of proteins known as "seripauperins" (29).…”

mentioning

confidence: 99%

Reciprocal Regulation of Anaerobic and Aerobic Cell Wall Mannoprotein Gene Expression in Saccharomyces cerevisiae

et al. 2001

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The DAN/TIR genes encode nine cell wall mannoproteins in Saccharomyces cerevisiae which are expressed during anaerobiosis (DAN1, DAN2, DAN3, DAN4, TIR1, TIR2, TIR3, TIR4, and TIP1). Most are expressed within an hour of an anaerobic shift, but DAN2 and DAN3 are expressed after about 3 h. At the same time, CWP1 and CWP2, the genes encoding the major mannoproteins, are down-regulated, suggesting that there is a programmed remodeling of the cell wall in which Cwp1 and Cwp2 are replaced by nine anaerobic counterparts. TIP1, TIR1, TIR2, and TIR4 are also induced during cold shock. Correspondingly, CWP1 is downregulated during cold shock. As reported elsewhere, Mox4 is a heme-inhibited activator, and Mot3 is a heme-induced repressor of the DAN/TIR genes (but not of TIP1). We show that CWP2 (but not CWP1) is controlled by the same factors, but in reverse fashion-primarily by Mot3 (which can function as either an activator or repressor) but also by Mox4, accounting for the reciprocal regulation of the two groups of genes. Disruptions of TIR1, TIR3, or TIR4 prevent anaerobic growth, indicating that each protein is essential for anaerobic adaptation. The Dan/Tir and Cwp proteins are homologous, with the greatest similarities shown within three subgroups: the Dan proteins, the Tip and Tir proteins, and, more distantly, the Cwp proteins. The clustering of homology corresponds to differences in expression: the Tip and Tir proteins are expressed during hypoxia and cold shock, the Dan proteins are more stringently repressed by oxygen and insensitive to cold shock, and the Cwp proteins are oppositely regulated by oxygen and temperature.The cell wall of Saccharomyces cerevisiae is a rigid structure which determines cell morphology and also serves as a protective barrier, providing mechanical protection and enabling selective uptake of macromolecules (1a, 4, 7). A major component of the cell wall is mannoprotein, comprising about 40% of its mass. Mannoproteins are believed to be determinants of cell wall permeability (31), and certain ones are also essential for developmental events such as mating and transition to hyphal growth (18,24). Some mannoproteins can be extracted from the cell wall with detergent; others are covalently bound but can be released with glucanase (7). Proteins in the latter category have common features, including a region rich in serine and threonine, a glycosylphosphatidylinositol (GPI) anchor attachment signal at C termini (3,8), and an endoplasmic reticulum localization sequence; several also have a PAU domain. This segment of about 100 amino acids is shared among a group of proteins known as "seripauperins" (29).The Cwp2 mannoprotein (28) is one of the most abundant proteins of the cell wall and is believed to play a role in its stabilization, along with another homologous constituent, Cwp1 (23, 27, 28). While Cwp1 and Cwp2 are expressed under normal growth conditions, other mannoproteins are expressed in response to environmental stress. The most extensive response is the induction of several homologou...

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“…The telomere-proximal domain consist of 0-4 repeats of Y' elements, which are highly conserved (98-99% sequence identity) across all chromosomes (Louis & Haber 1992). The telomere-distal domain contains sequence blocks that are only homologous to a few subtelomeres and includes gene families that function in the use of different carbon sources such as MAL (-glucosidase/maltose permease) and MEL (-glactosidase) (Carlson & Botstein 1983;Carlson et al 1985;Charron & Michels 1988;Charron et al 1989;Louis & Haber 1992;Naumov et al 1992;Ness & Aigle 1995;Turakainen et al 1993;Viswanathan et al 1994). …”

Section: Telomere and Subtelomere Recombinationmentioning

confidence: 99%

Telomere as an Important Player in Regulation of Microbial Pathogen Virulence

Li¹

2012

Reviews on Selected Topics of Telomere Biology

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Seripauperins of Saccharomyces cerevisiae: a new multigene family encoding serine-poor relatives of serine-rich proteins

Cited by 56 publications

References 8 publications

Insights on the Evolution of Metabolic Networks of Unicellular Translationally Biased Organisms from Transcriptomic Data and Sequence Analysis

Insights on the Evolution of Metabolic Networks of Unicellular Translationally Biased Organisms from Transcriptomic Data and Sequence Analysis

Reciprocal Regulation of Anaerobic and Aerobic Cell Wall Mannoprotein Gene Expression in Saccharomyces cerevisiae

Telomere as an Important Player in Regulation of Microbial Pathogen Virulence

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