Emergence of Species-Specific Transporters during Evolution of the Hemiascomycete Phylum

By De Hertogh, Benoît; Hancy, Frédéric et al. | Genetics, February 2006 | Go to article overview
Save to active project

Emergence of Species-Specific Transporters during Evolution of the Hemiascomycete Phylum


De Hertogh, Benoît, Hancy, Frédéric, Goffeau, André, Baret, Philippe V., Genetics


ABSTRACT

We have traced the evolution patterns of 2480 transmembrane transporters from five complete genome sequences spanning the entire Hemiascomycete phylum: Saccharomyces cerevisiae, Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, and Yarrowia lipolytica. The use of nonambiguous functional and phylogenetic criteria derived from the TCDB classification system has allowed the identification within the Hemiascomycete phylum of 97 small phylogenetic transporter subfamilies comprising a total of 355 transporters submitted to four distinct evolution patterns named "ubiquitous," "species specific," "phylum gains and losses," or "homoplasic." This analysis identifies the transporters that contribute to the emergence of species during the evolution of the Hemiascomycete phylum and may aid in establishing novel phylogenetic criteria for species classification.

THE Hemiascomycete yeasts are believed to have diverged from a common ancestral fungus at least 400 million years ago. This phylum comprises >1200 known species (KURTZMAN and FELL 1998; BOEKHOUT 2005). The first Hemiascomycete genome sequence, that of Saccharomyces cerevisiae, has unraveled the existence of >30% of duplicated genes. This observation led to the hypothesis of a recent whole-genome duplication of the Saccharomyces genome (PHILIPPSEN et al. 1997; WOLFE and SHIELDS 1997). A massive exploration of partially sequenced genomes from 13 Hemiascomycete species (SouciET et al. 2000) as well as the sequence comparison of a selected set of 40 duplicated gene sequences from six different species further investigated the origin of duplicated genes within the Hemiascomycete phylum (LANGKJAER et al. 2003). Analysis of several nearly complete genome sequences from Hemiascomycete species closely related to S. cerevisiae has dated the whole-genome duplication after the emergence of Kluyveromyces waltii (KELLIS et al. 2004), Ashbya gossypii (DIETRICH et al. 2004), and K. lactis (DujON et al. 2004) but before that of all sensus stricto and sensus lato Saccharomyces species (CLIFTEN et al. 2003; KELLIS et al. 2003) and Candida glabrata (DujON et al. 2004). Thèse data established the high frequency of gene loss among the duplicated genes. The existence in fungi of numerous gene duplication events followed by differential evolutionary drift of one of the two gene copies is believed to be a major force for adaptation to novel ecological niches and further speciation (OHNO 1970; KELLIS et al. 2003; LANGKJAER et al. 2003; DUJON et al. 2004).

The complete genome sequence of four species widely spread over the Hemiascomycete phylum became recently available: C. glabrata, the second most prominent causative agent of human fungal infection; K. lactis, a milk-loving yeast, believed to have diverged from the Saccharomyces clade at least 150 millions years ago; Debaromyces hansenii, a halotolerant species contaminating many dairy products; and Yarrowia lipolytica, a distantly related yeast that shares a number of properties with filamentous fungi (DujON et al. 2004). In the context of this Genolevures project, a uniform nomenclature was designed to facilitate comparisons between species (DURRENS and SHERMAN 2005). These data established that in addition to a recent whole-genome duplication, variable levels of segmentai duplication, tandem repeats, and other duplication events of still unknown mechanisms have occurred during evolution of the Hemiascomycete phylum. The analyses of more ancient genomes such as those from the major human Hemiascomycete pathogen C. albicans (JONES et al. 2004) and from the Euascomycete filamentous fungus Neurospora crassa (GALAGAN et al. 2003) are fully consistent with this view.

Most of the gene products and gene families analyzed so far concerned nonmembrane proteins or RNAs. We wish to focus our analysis here on the evolutionary fate of transmembrane transporter proteins that correspond to ~10% of the coding genes in the Hemiascomycete phylum.

The rest of this article is only available to active members of Questia

Sign up now for a free, 1-day trial and receive full access to:

  • Questia's entire collection
  • Automatic bibliography creation
  • More helpful research tools like notes, citations, and highlights
  • Ad-free environment

Already a member? Log in now.

Notes for this article

Add a new note
If you are trying to select text to create highlights or citations, remember that you must now click or tap on the first word, and then click or tap on the last word.
One moment ...
Project items

Items saved from this article

This article has been saved
Highlights (0)
Some of your highlights are legacy items.

Highlights saved before July 30, 2012 will not be displayed on their respective source pages.

You can easily re-create the highlights by opening the book page or article, selecting the text, and clicking “Highlight.”

Citations (0)
Some of your citations are legacy items.

Any citation created before July 30, 2012 will labeled as a “Cited page.” New citations will be saved as cited passages, pages or articles.

We also added the ability to view new citations from your projects or the book or article where you created them.

Notes (0)
Bookmarks (0)

You have no saved items from this article

Project items include:
  • Saved book/article
  • Highlights
  • Quotes/citations
  • Notes
  • Bookmarks
Notes
Cite this article

Cited article

Style
Citations are available only to our active members.
Sign up now to cite pages or passages in MLA, APA and Chicago citation styles.

(Einhorn, 1992, p. 25)

(Einhorn 25)

1

1. Lois J. Einhorn, Abraham Lincoln, the Orator: Penetrating the Lincoln Legend (Westport, CT: Greenwood Press, 1992), 25, http://www.questia.com/read/27419298.

Cited article

Emergence of Species-Specific Transporters during Evolution of the Hemiascomycete Phylum
Settings

Settings

Typeface
Text size Smaller Larger
Search within

Search within this article

Look up

Look up a word

  • Dictionary
  • Thesaurus
Please submit a word or phrase above.
Print this page

Print this page

Why can't I print more than one page at a time?

While we understand printed pages are helpful to our users, this limitation is necessary to help protect our publishers' copyrighted material and prevent its unlawful distribution. We are sorry for any inconvenience.
Full screen

matching results for page

Cited passage

Style
Citations are available only to our active members.
Sign up now to cite pages or passages in MLA, APA and Chicago citation styles.

"Portraying himself as an honest, ordinary person helped Lincoln identify with his audiences." (Einhorn, 1992, p. 25).

"Portraying himself as an honest, ordinary person helped Lincoln identify with his audiences." (Einhorn 25)

"Portraying himself as an honest, ordinary person helped Lincoln identify with his audiences."1

1. Lois J. Einhorn, Abraham Lincoln, the Orator: Penetrating the Lincoln Legend (Westport, CT: Greenwood Press, 1992), 25, http://www.questia.com/read/27419298.

Cited passage

Welcome to the new Questia Reader

The Questia Reader has been updated to provide you with an even better online reading experience.  It is now 100% Responsive, which means you can read our books and articles on any sized device you wish.  All of your favorite tools like notes, highlights, and citations are still here, but the way you select text has been updated to be easier to use, especially on touchscreen devices.  Here's how:

1. Click or tap the first word you want to select.
2. Click or tap the last word you want to select.

OK, got it!

Thanks for trying Questia!

Please continue trying out our research tools, but please note, full functionality is available only to our active members.

Your work will be lost once you leave this Web page.

For full access in an ad-free environment, sign up now for a FREE, 1-day trial.

Already a member? Log in now.