Alternative ribosomal protein RpmE2 is produced under zinc limitation in Neisseria gonorrhoeae and slows translation and bacterial growth

To enhance its pathogenic potential, Neisseria gonorrhoeae (Gc) pirates zinc from human metal sequestration proteins using TonB-dependent outer membrane transport systems. However, cytoplasmic mechanisms by which Gc adapts to zinc limitation are still uncharacterized. rpmE2 and rpmJ2 transcripts, encoding alternative L31 and L36 ribosomal proteins, respectively, which are not predicted to bind zinc, are significantly more abundant in zinc-limited Gc. In other bacterial species, alternative ribosomal proteins replace canonical zinc-binding ribosomal proteins when zinc availability is low, enabling growth under metal limitation. We found that Gc rpmE2 and rpmJ2 are in an operon and transcriptionally induced under zinc limitation by derepression via the zinc uptake regulator Zur, while genes encoding canonical proteins rpmE and rpmJ are not zinc-regulated. In contrast to other bacteria, ribosomes in zinc-limited Gc contained both RpmE2 and RpmE. Furthermore, Gc deleted for RpmE2 and RpmJ2 grew better than the wild-type parent under zinc limitation. Gc engineered to produce only RpmE2 exhibited a growth defect relative to RpmE-only Gc, regardless of zinc availability. Moreover, ribosomes from RpmE2-only Gc had reduced translation in vitro . Thus, unlike other bacteria, the alternative L31 protein RpmE2 is not functionally equivalent to the canonical RpmE in Gc. Instead, the ribosomes of zinc-limited Gc are heterogeneous, containing either alternative or canonical ribosomal proteins. We propose that L31 ribosomal protein alternation allows Gc to withstand zinc limitation by reducing translation and slowing growth, to prolong its survival when encountering host-imposed nutritional immunity. IMPORTANCE Zinc acquisition is crucial for growth and infectivity of Neisseria gonorrhoeae (Gc). However, research on Gc adaptation to zinc limitation has primarily focused on outer and inner membrane zinc transporters. Here, we implicate ribosomal protein alternation in the Gc response to zinc limitation. Ribosomes containing the non-zinc-binding, alternative ribosomal protein RpmE2 are less translationally active, and RpmE2-producing bacteria grow more slowly. This contrasts with reports from other bacteria, where ribosomal protein alternation facilitates growth in zinc-limited conditions. This work uncovers a new way in which ribosomal protein alternation enables bacterial resistance to nutritional immunity.