Oct2 transcription factor of a teleost fish: activation domains and function from an enhancer.
ABSTRACT Oct2 transcription factors of the catfish (Ictalurus punctatus) are expressed as alternatively spliced alpha and beta isoforms. Functional analysis revealed an N-terminal glutamine (Q)-rich transactivation domain common to both isoforms of catfish Oct2. A C-terminal proline, serine, threonine (PST)-rich activation domain was identified exclusively in the beta isoform. Activation domains of fish and mammalian Oct2 showed cell type- and species-specific activity correlated with their biochemical composition (Q-rich vs PST-rich). In contrast the activation domains of the aryl hydrocarbon receptor and aryl hydrocarbon receptor nuclear translocator of fish and mammals showed no correlation of activity with biochemical composition or species of origin. Although isolated catfish Oct2 activation domains were unable to drive transcription from a site 1.9kb distal to the promoter, Oct2beta activated transcription from both an IgH enhancer and an array of octamer motifs at this distal position. The properties of catfish Oct2 activation domains differ depending on whether they are studied in isolation or as components of the intact transcription factor.
- [show abstract] [hide abstract]
ABSTRACT: The Brazilian organic food sector has experienced important growth during the last two decades. Brazilian smallholders, however, are facing huge challenges to enter and benefit from this growth in a sustainable way. Combining the lens of New Institutional Economics and socio-anthropology, we analyse six experiences of Brazilian smallholders who converted to organics in the 1990s’. Three different food systems are featured in this analysis: an alternative food system, which is strongly interwoven with the Brazilian Agro-ecological movement and two commercial food procurement systems oriented towards domestic and an export markets driven mainly by supermarket chains. The analytical focus was on 1) the governance of these food systems, 2) the constraints farmers are facing within these food systems and, 3) the benefits that they can expect from market inclusion. We highlighted the roles that NGOs, Faith-based organisations and public-related agencies play in supporting the inclusion of smallholders into all three food systems. We confirmed the arguments in support of pursuing the agro-ecological development based model in Brazil, but underlined that there is a critical lack of support for famers included in the commercial market-oriented food systems. Such a lack is even more critical as the food systems driven by expanding supermarket chains are characterised by strong asymmetric power relations at the expense of smallholders. Considering the reluctance of NGOs and Faith-based organisations to support these farmers, we call for efforts to be made to provide a policy framework to enable public related entities to secure sustainable inclusion into these systems and exit strategies for those experiencing exclusion from these highly competitive food systems.Journal of Rural Studies - J RURAL STUD. 01/2012;
- [show abstract] [hide abstract]
ABSTRACT: The functional importance of variable, transcriptional regulatory sequences within and among natural populations is largely unexplored. We analysed the cytochrome P4501A (CYP1A) promoter in three populations of the minnow, Fundulus heteroclitus, because two SNPs in the promoter and first intron of CYP1A are under selection in populations adapted to pollutants. To define the importance of these SNPs, 1630 bp of the CYP1A promoter and first intron and exon were sequenced in eight individuals from three populations: a population from a polluted environment resistant to some aromatic pollutants and two flanking reference populations. CYP1A is induced by many aromatic pollutants, but in populations adapted to pollutants, CYP1A has been shown to be refractory to induction. We were interested in understanding whether variation in the CYP1A promoter explains mechanism(s) of adaptation to these aromatic pollutants. The CYP1A promoter was extremely variable (an average of 9.3% of the promoter nucleotides varied among all populations) and exhibited no fixed differences between populations. As CYP1A is poorly inducible in adapted fish, we hypothesized that CYP1A promoter regions might vary functionally between populations. Unexpectedly, in vitro analysis showed significantly greater transcription from CYP1A promoters found in the population from the polluted environment relative to promoters found in both reference populations. Thus, despite extensive variation among populations and lack of fixed differences between populations, individuals from a polluted environment have significantly enhanced promoter activity. These data demonstrate that intraspecific variation, which provides the raw material for natural selection to act on, can occur while maintaining promoter function.Molecular Ecology 11/2011; 20(24):5236-47. · 6.28 Impact Factor
- [show abstract] [hide abstract]
ABSTRACT: The immunoglobulin heavy chain locus of teleost fish is driven by an enhancer (Eμ3′) that contains, in all species examined, octamer and E-box motifs (typically μE5). Thus, the transcription factors known (through experiments in fish) or predicted (from knowledge of their mammalian homologues) to be involved in the function of the enhancer are the octamer-binding (Oct) transcription factors Oct1 and Oct2, their coactivator BOB.1 and the μE5-binding E-proteins (E2A, HEB and E2-2). Comparative genomic analysis of the genes encoding these transcription factors in teleost fish permits some conclusions to be drawn concerning the fate of these genes following the genome-wide duplication event that occurred in this lineage. Although problems in the assembly of some regions of the zebrafish genome may complicate the analysis, the pattern that emerges from these studies is that Oct1, Oct2, BOB.1 and E2-2 are all single-copy genes in teleosts, whereas in the case of E2A and HEB, two copies of each gene are present. The evolutionary conservation of sequences between related genes is variable, but with the highest similarities always being observed in the domains with ligand-binding function, whether the ligand is a DNA motif or, as in the case of BOB.1, another protein domain. A major challenge that must be faced is the assignment of precise functions to these diverse transcription factors in teleosts; assumptions drawn by inference from their mammalian homologues will likely be misleading.Journal of Fish Biology 09/2007; 71(sb):153 - 173. · 1.83 Impact Factor