Fernandes, GR

Guedes, RLM

Moura, LK

Ortega, JM

Prosdocimi, F

Ribeiro, HAL

BMC Genomics

English

PubMed

Abstract
          
            Background
            Besides being building blocks for proteins, amino acids are also key metabolic intermediates in living cells. Surprisingly a variety of organisms are incapable of synthesizing some of them, thus named Essential Amino Acids (EAAs). How certain ancestral organisms successfully competed for survival after losing key genes involved in amino acids anabolism remains an open question. Comparative genomics searches on current protein databases including sequences from both complete and incomplete genomes among diverse taxonomic groups help us to understand amino acids auxotrophy distribution.
          
          
            Results
            Here, we applied a methodology based on clustering of homologous genes to seed sequences from autotrophic organisms Saccharomyces cerevisiae (yeast) and Arabidopsis thaliana (plant). Thus we depict evidences of presence/absence of EAA biosynthetic and nitrogen assimilation enzymes at phyla level. Results show broad loss of the phenotype of EAAs biosynthesis in several groups of eukaryotes, followed by multiple secondary gene losses. A subsequent inability for nitrogen assimilation is observed in derived metazoans.
          
          
            Conclusions
            A Great Deletion model is proposed here as a broad phenomenon generating the phenotype of amino acids essentiality followed, in metazoans, by organic nitrogen dependency. This phenomenon is probably associated to a relaxed selective pressure conferred by heterotrophy and, taking advantage of available homologous clustering tools, a complete and updated picture of it is provided.
          </jats:sec

RLM Guedes

F Prosdocimi

GR Fernandes

LK Moura

HAL Ribeiro

JM Ortega

Crossref

Amino acids biosynthesis and nitrogen assimilation pathways: a great genomic deletion during eukaryotes evolution

A Prokaryotic Gene Cluster Involved in Synthesis of Lysine through the Amino Adipate Pathway: A Key to the Evolution of Amino Acid Biosynthesis. Genome Research

A: Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes.

al: A procedure to recruit members to enlarge protein family databases– the building of UECOG (UniRef-Enriched COG Database) as a model. Genetics and molecular research GMR

Amino acid requirements in humans: with a special emphasis on the metabolic availability of amino acids. Amino Acids

An algorithm for progressive multiple alignment of sequences with insertions.

Energy costs of protein and fatty acid synthesis.

Essential amino acid usage and evolutionary nutrigenomics of eukaryotes–insights into the differential usage of amino acids in protein domains and extra-domains. Genetics and molecular research GMR

et al: The COG database: an updated version includes eukaryotes.

Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature

Hedges SB: Evolutionary sequence analysis of complete eukaryote genomes.

JM: A set of amino acids found to occur more frequently in human and fly than in plant and yeast proteomes consists of non-essential amino acids.

JM: Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence.

KEGG: From genes to biochemical pathways. Bioinfomatics: Databases and Systems

Lazcano A: Molecular Evolution of the Lysine Biosynthetic Pathways.

Lecointre G: Early steps of metabolism evolution inferred by cladistic analysis of amino acid catabolic pathways. Comptes Rendus Biologies

Lecointre G: Ordering events of biochemical evolution. Biochimie

Leustek T: Biosynthesis of lysine in plants: evidence for a variant of the known bacterial pathways. Biochim Biophys Acta

M: α-Aminoadipate aminotransferase from an extremely thermophilic bacterium, Thermus thermophilus.

Metabolic Demands for Amino Acids and the Human Dietary Requirement: Millward and Rivers

Orthology, paralogy and proposed classification for paralog subtypes. Trends in Genetics

S: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Molecular Biology and Evolution

T: Energy cost of whole-body protein synthesis measured in vivo in chicks. Comp Biochem Physiol A Comp Physiol

The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution. Genome Biol

The KEGG resource for deciphering the genome. Nucleic Acids Research

The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution

The nutritional role of indispensable amino acids and the metabolic basis for their requirements.

The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Research

TJ: Evolution of Glutamate Dehydrogenase Regulation of Insulin Homeostasis Is an Example of Molecular Exaptation†. Biochemistry

UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics

WF: Retention and Loss of Amino Acid Biosynthetic Pathways Based on Analysis of Whole-Genome Sequences. Eukaryotic Cell

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3287585

Amino acids biosynthesis and nitrogen assimilation pathways: a great genomic deletion during eukaryotes evolution

Abstract

Similar works

Full text

Available Versions

Crossref