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

Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, MG, Brazil.
BMC Genomics (Impact Factor: 3.99). 12/2011; 12 Suppl 4(Suppl 4):S2. DOI: 10.1186/1471-2164-12-S4-S2
Source: PubMed

ABSTRACT 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.
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.
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.

Download full-text


Available from: Francisco Prosdocimi, Sep 28, 2015
32 Reads
  • Source
    • "See Table S4, lines 14–30, for full protein names, UniProt accession numbers, and transcript numbers. methionine is an amino acid essential in the diet) (Guedes et al. 2011) but surprisingly inconsistent with labeling results indicating synthesis of methionine by starved aposymbiotic anemones (Wang and Douglas 1999). A related puzzle is that the Aiptasia transcriptome and the A. digitifera genome appear to contain genes encoding both a homoserine O-acetyltransferase and a cystathionine g-synthase, which would allow the synthesis of cystathionine from homoserine (Figure 5), but not a cystathionine b-lyase, which in many microorganisms is responsible for the synthesis of homocysteine from cystathionine (Table S5, lines 18–20). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Coral reefs provide habitats for a disproportionate number of marine species relative to the small area of the oceans that they occupy. The mutualism between the cnidarian animal hosts and their intracellular dinoflagellate symbionts provides the nutritional foundation for coral growth and formation of reef structures, as algal photosynthesis can provide >90% of the host's total energy. Disruption of this symbiosis ("coral bleaching") is occurring on a large scale due primarily to anthropogenic factors and poses a major threat to the future of coral reefs. Despite the importance of this symbiosis, the cellular mechanisms involved in its establishment, maintenance, and breakdown remain largely unknown. Here we report our continued development of genomic tools to study these mechanisms in Aiptasia, a small sea anemone with great promise as a model system for studies of cnidarian-dinoflagellate symbiosis. Specifically, we have generated de novo assemblies of the transcriptomes of both a clonal line of symbiotic anemones and their endogenous dinoflagellate symbionts. We then compared transcript abundances in animals with and without dinoflagellates. This analysis identified >900 differentially expressed genes and allowed us to generate testable hypotheses about the cellular functions affected by symbiosis establishment. The differentially regulated transcripts include >60 encoding proteins that may play roles in transporting various nutrients between the symbiotic partners; many more encoding proteins functioning in several metabolic pathways, providing clues as to how the transported nutrients may be used by the partners; and several encoding proteins that may be involved in host recognition and tolerance of the dinoflagellate.
    G3-Genes Genomes Genetics 12/2013; 4(2). DOI:10.1534/g3.113.009084 · 3.20 Impact Factor
  • Source
    • "For anabolic biochemistry, the biosynthesis of heme, nucleotides and multiple coenzymes is undertaken by many unicellular and multicellular eukaryotes. In contrast, biosynthetic pathways leading to the ''essential'' amino acids have been lost from animals and many taxonomically diverse protists (Guedes et al., 2011; Payne & Loomis, 2006). The latter organisms tend to be either phagotrophs or parasites. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Abstract Eukaryogenesis, the origin of the eukaryotic cell, represents one of the fundamental evolutionary transitions in the history of life on earth. This event, which is estimated to have occurred over one billion years ago, remains rather poorly understood. While some well-validated examples of fossil microbial eukaryotes for this time frame have been described, these can provide only basic morphology and the molecular machinery present in these organisms has remained unknown. Complete and partial genomic information has begun to fill this gap, and is being used to trace proteins and cellular traits to their roots and to provide unprecedented levels of resolution of structures, metabolic pathways and capabilities of organisms at these earliest points within the eukaryotic lineage. This is essentially allowing a molecular paleontology. What has emerged from these studies is spectacular cellular complexity prior to expansion of the eukaryotic lineages. Multiple reconstructed cellular systems indicate a very sophisticated biology, which by implication arose following the initial eukaryogenesis event but prior to eukaryotic radiation and provides a challenge in terms of explaining how these early eukaryotes arose and in understanding how they lived. Here, we provide brief overviews of several cellular systems and the major emerging conclusions, together with predictions for subsequent directions in evolution leading to extant taxa. We also consider what these reconstructions suggest about the life styles and capabilities of these earliest eukaryotes and the period of evolution between the radiation of eukaryotes and the eukaryogenesis event itself.
    Critical Reviews in Biochemistry and Molecular Biology 07/2013; 48(4):373-396. DOI:10.3109/10409238.2013.821444 · 7.71 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Secondary metabolites are ubiquitous in bacteria, but by definition, they are thought to be nonessential. Highly toxic secondary metabolites such as patellazoles have been isolated from marine tunicates, where their exceptional potency and abundance implies a role in chemical defense, but their biological source is unknown. Here, we describe the association of the tunicate Lissoclinum patella with a symbiotic α-proteobacterium, Candidatus Endolissoclinum faulkneri, and present chemical and biological evidence that the bacterium synthesizes patellazoles. We sequenced and assembled the complete Ca. E. faulkneri genome, directly from metagenomic DNA obtained from the tunicate, where it accounted for 0.6% of sequence data. We show that the large patellazoles biosynthetic pathway is maintained, whereas the remainder of the genome is undergoing extensive streamlining to eliminate unneeded genes. The preservation of this pathway in streamlined bacteria demonstrates that secondary metabolism is an essential component of the symbiotic interaction.
    Proceedings of the National Academy of Sciences 11/2012; 109(50). DOI:10.1073/pnas.1213820109 · 9.67 Impact Factor
Show more