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Background  Gene duplication and the subsequent divergence of paralogous pairs play a central role in the evolution of novel gene functions.  S. cerevisiae  possesses two paralogous genes ( ALT1/ALT2 ) which presumably encode alanine aminotransferases. It has been previously shown that Alt1 encodes an alanine aminotransferase, involved in alanine metabolism; however the physiological role of Alt2 is not known. Here we investigate whether  ALT2  encodes an active alanine aminotransferase.    Principal Findings  Our results show that although  ALT1  and  ALT2  encode 65% identical proteins, only Alt1 displays alanine aminotransferase activity; in contrast  ALT2  encodes a catalytically inert protein.  ALT1  and  ALT2  expression is modulated by Nrg1 and by the intracellular alanine pool.  ALT1  is alanine-induced showing a regulatory profile of a gene encoding an enzyme involved in amino acid catabolism, in agreement with the fact that Alt1 is the sole pathway for alanine catabolism present in  S. cerevisiae . Conversely,  ALT2  expression is alanine-repressed, indicating a role in alanine biosynthesis, although the encoded-protein has no alanine aminotransferase enzymatic activity. In the ancestral-like yeast  L. kluyveri , the alanine aminotransferase activity was higher in the presence of alanine than in the presence of ammonium, suggesting that as for  ALT1 ,  LkALT1  expression could be alanine-induced.  ALT2  retention poses the questions of whether the encoded protein plays a particular function, and if this function was present in the ancestral gene. It could be hypotesized that  ALT2  diverged after duplication, through neo-functionalization or that  ALT2  function was present in the ancestral gene, with a yet undiscovered function.    Conclusions    ALT1  and  ALT2  divergence has resulted in delegation of alanine aminotransferase activity to Alt1. These genes display opposed regulatory profiles:  ALT1  is alanine-induced, while  ALT2  is alanine repressed. Both genes are negatively regulated by the Nrg1 repressor. Presented results indicate that alanine could act as  ALT2  Nrg1-co-repressor.

Paralogous ALT1 and ALT2 Retention and Diversification Have Generated Catalytically Active and Inactive Aminotransferases in Saccharomyces cerevisiae