Bacterial protein secretion is a central process that substantially contributes to fitness and survival. We recently revealed distinctive features of secretion complexes in cyanobacteria, globally prevalent photosynthetic prokaryotes that significantly contribute to primary production. Our studies of a biofilm self-suppression mechanism that operates in the cyanobacterium Synechococcus elongatus uncovered two components required for cyanobacterial protein secretion: The RNA-chaperone Hfq and a protein annotated `hypothetical` which we denote EbsA (essential for biofilm self-suppression A). EbsA homologs are highly conserved and widespread in diverse cyanobacteria but are not found outside this clade. We revealed a tripartite complex of EbsA, Hfq and the ATPase homolog T2SE and demonstrated that either one of these components is required for assembly of the hair-like appendages; type 4 pili, and for DNA competence, in addition to their role in protein secretion and biofilm self-suppression. NMR structure of EbsA indicates some similarity to chaperones of type 3 systems; however, such injectisome machinery was not identified in cyanobacteria. Additionally, EbsA is structurally similar to subunit 14 of yeast signal recognition particles. Together, these data suggest unique characteristics of S. elongatus secretion, pilus assembly and DNA uptake complexes. A phenotype resulting from impairment of the EbsA-homolog in the cyanobacterium Synechocystis PCC 6803 suggests that these features are a general cyanobacterial trait.