Classification of all putative permeases and other membrane multispanners of the Major Facilitator Superfamily encoded by the complete genome of Saccharomyces cerevisiae

 

FEMS Microbiol Rev. 21(2): 113-134 (1997)

 

Bart Nelissen
Departement Biochemie, Universiteit Antwerpen (UIA), Universiteitsplein 1, B-2610 Antwerpen, Belgium
Present address: Experimental Molecular Biology, Janssen Research Foundation, Division of Janssen Pharmaceutica N.V., B-2340 Beerse, Belgium, Fax: (32) (14) 60 61 11, E-mail: bnelisse@janbe.jnj.com

Rupert De Wachter
Departement Biochemie, Universiteit Antwerpen (UIA), Universiteitsplein 1, B-2610 Antwerpen, Belgium
Fax: (32) (3) 820 22 48
E-mail: dwachter@uia.ua.ac.be

André Goffeau*
Unité de Biochimie Physiologique, Faculté des Sciences Agronomiques, Université Catholique de Louvain, Place Croix du Sud 2/20, B-1348 Louvain-la-Neuve, Belgium
Fax: (32) (10) 47 38 72
E-mail: goffeau@fysa.ucl.ac.be

* Corresponding author, to whom reprint requests should be sent.

Abstract

On the basis of the complete genome sequence of the budding yeast Saccharomyces cerevisiae, a computer-aided analysis was carried out of all members of the Major Facilitator Superfamily or MFS, which consists of permeases with 12 transmembrane spans. Binary sequence comparisons of all 5885 open reading frames predicted to be encoded by the yeast genome resulted in the detection of 186 potential MFS proteins of which 149 could be clustered into 23 families. Putative permease functions could be assigned to 12 families, the largest including sugar, amino acid, and multidrug transport. Phylogenetic clustering of proteins with a known function to proteins with an unknown function, allowed to predict a possible permease function for new membrane proteins, resulting in a total of 119 proteins with known function. Multiple sequence alignments were made for all families, and evolutionary trees were constructed for families with at least four members. The latter resulted in the identification of subclusters within several families. No functional clues were predicted for 41 proteins among which 21 proteins could be clustered in 7 new families of unknown permease function, while 17 other proteins with a potential permease function were unclustered.

Major Facilitator Family

Evolutionary relationship

Sugar permease homologues

Evolutionary tree

Amino acid permease homologues

Evolutionary tree

Multidrug permease homologues, family 1

Evolutionary tree

Multidrug permease homologues, family 2

Evolutionary tree

Allantoate permease homologues

Evolutionary tree

Uracil/uridin/allantoin permease homologues

Evolutionary tree

Monocarboxylate permease homologues

Evolutionary tree

Sulfate permease homologues

Evolutionary tree

Ammonia permease homologues

 

Phosphate permease homologues

 

Purine/cytosine permease homologues

 

Calcium permease homologues

 

ER protein-translocation homologues

 

Vanadate-resistance protein homologues

 

Spore formation protein homologues

 

Sexual differentiation protein homologues

 

Unknown function

Evolutionary tree family 1
Evolutionary tree family 2

Single proteins with transport related functions

 

Single proteins with an unknown permease function

 

Single proteins with a potential permease function associated to other enzymatic functions