Genetic diversity of 16S rRNA and mcrA genes from methanogenic archaeas

Methanogenic archaeas are found in aquatic and terrestrial environments and are fundamental in the conversion of organic matter into methane, a gas that has a potential use as renewable source of energy, which is also considered as one of the main agents of the greenhouse effect. The vast majority of microbial genomes can be identified by a conservative molecular marker, the 16S ribosomal gene. However, the mcrA gene have been using in studies of methanogenic archaea diversity as an alternative marker, highly conserved and present only in methanogens. This gene allows the expression of the enzyme Methyl-coenzyme M reductase, the main agent in converting by-products of anaerobic digestion into methane. In this context, we aimed to study the genetic diversity of mcrA and 16S rRNA genes sequences available in databases. The nucleotide sequences were selected from the NCBI. The heterozygosity and molecular diversity indexes were calculated using the Arlequin 3.5 software, with plots generated by package R v3.0. The diversity and heterozygosity indices for both genes may have been influenced by the number and size of the sequences. Descriptive analysis of genetic diversity generated by sequences deposited in databases allowed a detailed study of these molecules. It is known that the organisms in a population are genetically distinct, and that, despite having similarities in their gene composition, the differences are essential for their adaptation to different environments.

Genetic diversity of 16S rRNA and mcrA genes from methanogenic archaeas

Methanogenic archaeas are found in aquatic and terrestrial environments and are fundamental in the conversion of organic matter into methane, a gas that has a potential use as renewable source of energy, which is also considered as one of the main agents of the greenhouse effect. The vast majority of microbial genomes can be identified by a conservative molecular marker, the 16S ribosomal gene. However, the mcrA gene have been using in studies of methanogenic archaea diversity as an alternative marker, highly conserved and present only in methanogens. This gene allows the expression of the enzyme Methyl-coenzyme M reductase, the main agent in converting by-products of anaerobic digestion into methane. In this context, we aimed to study the genetic diversity of mcrA and 16S rRNA genes sequences available in databases. The nucleotide sequences were selected from the NCBI. The heterozygosity and molecular diversity indexes were calculated using the Arlequin 3.5 software, with plots generated by package R v3.0. The diversity and heterozygosity indices for both genes may have been influenced by the number and size of the sequences. Descriptive analysis of genetic diversity generated by sequences deposited in databases allowed a detailed study of these molecules. It is known that the organisms in a population are genetically distinct, and that, despite having similarities in their gene composition, the differences are essential for their adaptation to different environments.(AU)

Prediction of mutations on structure primase of the archaeon Sulfolobus solfataricus / Predição de mutações na estrutura da primase da arquea Sulfolobus solfataricus

All living organisms need a DNA replication mechanism and it has been conserved in the three domains of life throughout evolutionary process. Primase is the enzyme responsible for synthesizing de novo RNA primers in DNA replication. Archaeo-Eukaryotic Primase (AEP) is the superfamily that typically forms a heterodimeric complex containing both a small catalytic subunit (PriS) and a large accessory noncatalytic subunit (PriL). Sulfolobus solfataricus is a model organism for research on the Genetics field. The aim of this work was to evaluate, via Bioinformatics tools, three mutations in the large subunit (PriL) of the archaeon Sulfolobus solfataricus. The aspartic acid residue in the positions (Asp) 62, (Asp) 235, (Asp) 241 have been substituted by glutamic acid (Glu). The highest positive free energy variation of the three substitutions analyzed occurred with the mutation at the (Asp) 241 site. The in silico analysis suggested that these mutations in PriL may destabilize its tridimensional structure interfering with replication mechanisms of Sulfolobus solfataricus. Moreover, it may also alter interactions with other molecules, making salt bridges, for instance.(AU)

Todos os organismos vivos necessitam de um eficiente mecanismo de replicação de DNA. Aolongo da evolução biológica foi observado que esse mecanismo é conservado nos três domínios da vida.Uma enzima importante que participa desse mecanismo é a RNA primase, a qual é responsável pela síntesede novo de iniciadores de RNA na replicação do DNA. Em Arquea-Eucariota, RNA Primase (AEP)tipicamente forma um complexo heterodimérico, que contém uma pequena subunidade catalítica (PriS) euma subunidade maior não catalítica acessória (PriL). Sulfolobus solfataricus é um organismo modelo deArquea para a pesquisa no campo da genética. O objetivo deste trabalho foi avaliar, por meio de ferramentasde bioinformática, três mutações pontuais na subunidade maior (PriL) de Sulfolobus solfataricus. Nassequências mutantes, os resíduos de ácido aspártico nas posições (Asp) 62, (Asp) 235, (Asp) 241 foramsubstituídos por ácido glutâmico (Glu). A maior variação de energia livre positiva das três mutaçõesanalisadas ocorreu no sítio (Asp) 241. A análise in silico sugeriu que essas mutações em PriL podemdesestabilizar sua estrutura tridimensional, interferindo com os mecanismos de replicação de Sulfolobussolfataricus. Além disso, podem alterar interações com outras moléculas, formando pontes salinas.(AU)