Methods and compositions are provided to improve nitrogen use efficiency in plants or plant parts, increase carbon fixation in a plant or plant part, increase grain yield or biomass production of the plant, and/or increase the stress tolerance of the plant. The compositions and methods of the invention modulate these various phenotypes by modulating the level of at least one Dof (for DNA binding with one finger) polypeptide having a Dof domain or a biologically active variant or fragment of a Dof domain.