The zinc-finger bearing xenogeneic silencer MucR in α-proteobacteria balances adaptation and regulatory integrity

Abstract

Foreign AT-rich genes drive bacterial adaptation to new niches while challenging the existing regulation network. Here we report that MucR, a conserved regulator in α-proteobacteria, balances adaptation and regulatory integrity in Sinorhizobium fredii, a facultative microsymbiont of legumes. Chromatin immunoprecipitation sequencing coupled with transcriptomic data reveal that average transcription levels of both target and non-target genes, under free-living and symbiotic conditions, increase with their conservation levels. Targets involved in environmental adaptation and symbiosis belong to genus or species core and can be repressed or activated by MucR in a condition-dependent manner, implying regulatory integrations. However, most targets are enriched in strain-specific genes of lower expression levels and higher AT%. Within each conservation levels, targets have higher AT% and average transcription levels than non-target genes and can be further up-regulated in the mucR mutant. This is consistent with higher AT% of spacers between −35 and −10 elements of promoters for target genes, which enhances transcription. The MucR recruitment level linearly increases with AT% and the number of a flexible pattern (with periodic repeats of Ts) of target sequences. Collectively, MucR directly represses AT-rich foreign genes with predisposed high transcription potential while progressive erosions of its target sites facilitate regulatory integrations of foreign genes.

Intracellular common gardens reveal niche differentiation in transposable element community during bacterial adaptive evolution

“…SF2 has two mucR copies with mucR1 and mucR2 in the Ch and pA replicons, respectively. They are 100% identical to their homologs characterized previously in S. fredii CCBAU45436 [29,47]. Here we further investigated to what extent the interactions between IS community and xenogeneic PsacB-sacB can be modulated by xenogeneic silencer MucR.…”

“…S5). The pA replicon is enriched with periodic Ts bound by the xenogeneic silencer MucR in S. fredii [29], and another convergent well-known xenogeneic silencer H-NS promotes transposition of various transposable elements such as Tn10, Tn5, Tn552, and IS903 in Gammaproteobacteria [43][44][45][46]. SF2 has two mucR copies with mucR1 and mucR2 in the Ch and pA replicons, respectively.…”

The Ros/MucR Zinc-Finger Protein Family in Bacteria: Structure and Functions

“…Recently, Jiao and colleagues [ 93 ] have performed very interesting analyses using ChIP-seq coupled with transcriptomic data, whose purpose was establishing the function of MucR as a global xenogeneic silencer and its potential role in the adaptive regulation of foreign genes. The adaptive regulation of MucR target genes belonging to individual pangenome subsets with different conservation levels (i.e., from genus core to strain-specific genes) or replicons (i.e., chromosome, chromid, symbiotic plasmid, and two smaller accessory plasmids) was investigated in the wild-type CCBAU45436 and the mucR mutant in free-living and symbiotic conditions [ 93 ]. These analyses confirmed that MucR1 is a global DNA-binding protein in S. fredii since, in total, 1350 genes were the target genes for this regulatory protein (1307 and 911 genes were found in free-living cells and bacteroid cells, respectively, and 868 genes were shared by these two conditions) ( Figure 3 ).…”

“…Moreover, the AT% of target genes was generally higher than that of non-target genes within individual replicons or core/accessory subsets of different conservation levels (ranging from genus core to strain-specific genes). High AT% is a characteristic feature of foreign genes in Proteobacteria ; thus, the results obtained by Jiao and others in 2021 [ 93 ] indicate MucR1 as a global regulator associated with foreign genes on different replicons and across different conservation levels. These authors showed that the higher conservation status of an S. fredii gene was accompanied by its lower AT content and a higher transcription level.…”

Copper (I) or (II) Replacement of the Structural Zinc Ion in the Prokaryotic Zinc Finger Ros Does Not Result in a Functional Domain

“…The presence of a structural zinc ion coordinated by the side chains of two cysteines and two histidines is crucial for the structural stability of this protein and is determinant in its folding process [ 30 , 31 , 32 ]. As the histidine imidazole and the cysteine thiolate belong to the array of amino acid functional groups more commonly found to bind copper ions in the cell [ 21 ], Ros87 represents an excellent model for our biophysical binding/folding investigation [ 33 , 34 , 35 , 36 , 37 , 38 ]. Our work aimed at contributing to the study of factors that convey the metal-binding selectivity in proteins and the deleterious effects of toxic metals on metallo-proteins [ 39 ].…”