Gene regulation at the transcriptional level is a central process in all organisms, and DNA-binding transcription factors, known as TFs, play a fundamental role. This class of proteins usually binds at specific DNA sequences, activating or repressing gene expression. In general, TFs are composed of two domains: the DNA-binding domain (DBD) and an extra domain, which in this work we have named “companion domain” (CD). This latter could be involved in one or more functions such as ligand binding, protein-protein interactions or even with enzymatic activity. In contrast to DBDs, which have been widely characterized both experimentally and bioinformatically, information on the abundance, distribution, variability and possible role of the CDs is scarce. Here, we investigated these issues associated with the domain architectures of TFs in prokaryotic genomes. To this end, 19 families of TFs in 761 non-redundant bacterial and archaeal genomes were evaluated. In this regard we found four main groups based on the abundance and distribution in the analyzed genomes: i) LysR and TetR/AcrR; ii) AraC/XylS, SinR, and others; iii) Lrp, Fis, ArsR, and others; and iv) a group that included only two families, ArgR and BirA. Based on a classification of the organisms according to the life-styles, a major abundance of regulatory families in free-living organisms, in contrast with pathogenic, extremophilic or intracellular organisms, was identified. Finally, the protein architecture diversity associated to the 19 families considering a weight score for domain promiscuity evidenced which regulatory families were characterized by either a large diversity of CDs, here named as “promiscuous” families given the elevated number of variable domains found in those TFs, or a low diversity of CDs. Altogether this information helped us to understand the diversity and distribution of the 19 Prokaryotes TF families. Moreover, initial steps were taken to comprehend the variability of the extra domain in those TFs, which eventually might assist in evolutionary and functional studies.
Extensive genomic studies on gene duplication in model organisms such as Escherichia coli and Saccharomyces cerevisiae have recently been undertaken. In these models, it is commonly considered that a duplication event may include a transcription factor (TF), a target gene, or both. Following a gene duplication episode, varying scenarios have been postulated to describe the evolution of the regulatory network. However, in most of these, the TFs have emerged as the most important and in some cases the only factor shaping the regulatory network as the organism responds to a natural selection process, in order to fulfil its metabolic needs. Recent findings concerning the regulatory role played by elements other than TFs have indicated the need to reassess these early models. Thus, we performed an exhaustive review of paralogous gene regulation in E. coli and Bacillus subtilis based on published information, available in the NCBI PubMed database and in well-established regulatory databases. Our survey reinforces the notion that despite TFs being the most prominent components shaping the regulatory networks, other elements are also important. These include small RNAs, riboswitches, RNA-binding proteins, sigma factors, protein-protein interactions and DNA supercoiling, which modulate the expression of genes involved in particular metabolic processes or induce a more complex response in terms of the regulatory networks of paralogous genes in an integrated interplay with TFs. IntroductionGene duplication is one of the main sources of functional divergence in organisms (Babu et al., 2004;Conant & Wolfe, 2008;Gelfand, 2006;Lynch & Conery, 2000;Teichmann & Babu, 2004). In order to fulfil an organism's metabolic needs, selection processes modify the regulation of the paralogous gene copies, taking advantage of a repertoire of new functions. Duplication events may include genes coding for transcription factors (TFs), permitting a more versatile adaptation of the functional diversity gained from the duplication of structural genes. Different aspects of the evolution of the regulatory networks of paralogous genes have been examined, including the co-evolution of the upstream regulatory regions and their corresponding TFs; the likely consequences of gain, loss, and replacement of TFs in the regulatory networks of paralogous genes (Gelfand, 2006;Teichmann & Babu, 2004); and also the topological and dynamic properties of the regulatory networks (Babu et al., 2006;Balaji et al., 2007; Luscombe et al., 2004). This review will consider the fascinating repertoire of additional mechanisms other than TFs, which help regulate the expression of paralogous genes in Escherichia coli and Bacillus subtilis. This analysis is derived from an extensive compilation of the regulatory information available from the NCBI PubMed database and deposited in the E. TFs are essential elements in the regulatory networks of paralogous genes TFs are the most prominent and usually the only regulatory element taken into account in any of the aforementioned stu...
BackgroundThe regulation of gene expression at the transcriptional level is a fundamental process in prokaryotes. Among the different kind of mechanisms modulating gene transcription, the one based on DNA binding transcription factors, is the most extensively studied and the results, for a great number of model organisms, have been compiled making it possible the in silico construction of their corresponding transcriptional regulatory networks and the analysis of the biological relationships of the components of these intricate networks, that allows to elucidate the significant aspects of their organization and evolution.ResultsWe present a thorough review of each regulatory element that constitutes the transcriptional regulatory network of Bacillus subtilis. For facilitating the discussion, we organized the network in topological modules. Our study highlight the importance of σ factors, some of them acting as master regulators which characterize modules by inter- or intra-connecting them and play a key role in the cascades that define relevant cellular processes in this organism. We discussed that some particular functions were distributed in more than one module and that some modules contained more than one related function. We confirm that the presence of paralogous proteins confers advantages to B. subtilis to adapt and select strategies to successfully face the extreme and changing environmental conditions in which it lives.ConclusionsThe intricate organization is the product of a non-random network evolution that primarily follows a hierarchical organization based on the presence of transcription and σ factor, which is reflected in the connections that exist within and between modules.
The Pelibuey sheep has adaptability to climatic variations, resistance to parasites, and good maternal ability, whereas some ewes present multiple births, which increases the litter size in farm sheep. The litter size in some wool sheep breeds is associated with the presence of mutations, mainly in the family of the transforming growth factor β (TGF-β) genes. To explore genetic mechanisms underlying the variation in litter size, we conducted a genome-wide association study in two groups of Pelibuey sheep (multiparous sheep with two lambs per birth vs. uniparous sheep with a single lamb at birth) using the OvineSNP50 BeadChip. We identified a total of 57 putative SNPs markers (p < 3.0 × 10−3, Bonferroni correction). The candidate genes that may be associated with litter size in Pelibuey sheep are CLSTN2, MTMR2, DLG1, CGA, ABCG5, TRPM6, and HTR1E. Genomic regions were also identified that contain three quantitative trait loci (QTLs) for aseasonal reproduction (ASREP), milk yield (MY), and body weight (BW). These results allowed us to identify SNPs associated with genes that could be involved in the reproductive process related to prolificacy.
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