Nitric oxide (NO) is an important biological messenger in living organisms, involved in numerous physiological processes. Particularly, it has been shown that NO performs a vital role in the adaptive response of plants facing pathogens. During the past several years, our team demonstrated that NO is rapidly produced and acts as a signaling compound in plant cells challenged by elicitors of plant defense. One major challenge is to determine how the correct specific response is evoked, despite shared use of the NO signal and, in some cases, its downstream second messengers. Here, we will present and discuss two mechanisms by which NO exerts its effects. First, part of NO biological functions could arise as a direct consequence of chemical reactions between NO and/or its derivatives with target proteins. Using a proteomic approach, we identified several proteins modified post-translationally by NO though S-nitrosylation in response to cryptogein, an elicitor of the tobacco defense responses. This include CDC48 CDC48 (cell division cycle 48), a member of the AAA+ ATPase (ATPase associated with various cellular activities) family acting as a chaperone-like protein. Functional analysis showed that NO inhibits CDC48 ATPase activity and triggers local conformational changes within the protein. Second, NO also controls physiological processes by modifying gene transcription. In this context, we have identified a network of genes regulated by NO endogenously produced in response to oligogalacturonides (OGs) in Arabidopsis thalianaleaf tissues using whole genome transcript analyses. Our analysis has pointed out the different cellular processes modulated by NO at the transcriptional level involved in plant resistance.