Macromolecular crowding links ribosomal protein gene dosage to growth rate inVibrio cholerae

Abstract

16 17 18 Text without Abstract, acknowledgments and legends.Abstract: Ribosomal protein (RP) genes locate near the replication origin (oriC) in fast- 27 growing bacteria, which is thought to have been selected as a translation optimization strategy. 28 Relocation of S10-spc-α locus (S10), which codes for most of the RP, to ectopic genomic 29 positions shows that its relative distance to the oriC correlates to a reduction on its dosage, its 30 expression, and bacterial growth rate. Deep-sequencing revealed that S10 relocation altered 31 chromosomal replication dynamics and genome-wide transcription. Such changes increased as 32 a function of oriC-S10 distance. Strikingly, in this work we observed that protein production 33 capacity was independent of S10 position. Since RP constitute a large proportion of cell mass, 34 lower S10 dosage could lead to changes in macromolecular crowding, impacting cell 35 physiology. Accordingly, cytoplasm fluidity was higher in mutants where S10 is most distant 36 from oriC. In hyperosmotic conditions, when crowding differences are minimized, the growth 37 rate and replication dynamics were highly alleviated in these strains. Therefore, on top of its 38 essential function in translation, RP genomic location contributes to sustain optimal 39 macromolecular crowding. This is a novel mechanism coordinating DNA replication with 40 bacterial growth. 41Introduction: 42 Replication, gene expression and segregation are tightly coordinated with the cell cycle to 43 preserve homeostasis (1, 2). Genome structure is a plausible factor contributing to integrate 44 these many simultaneous processes occurring on the same template. The relative simplicity and 45 the increasing amount of available data render bacterial genomes ideal models to study this 46 subject (3-6). 47Bacterial chromosomes are highly variable in their gene content, but highly conserved in terms 48 of the order of core genes in the chromosomes. Replication begins at a sole replication origin 49 (oriC), proceeding bidirectionally along two equally sized replichores until the terminal region 50 (ter). This organizes the genome along an ori-ter axis that interplays with cell physiology (Fig. 51 1a) (4, 5, 7). For instance, essential genes are overrepresented in the replicative leading strand 52 to avoid head-on collisions between the replication and transcription machineries (8). Large 53 inversions occur preferentially symmetrically with respect to the ori-ter axis to avoid the 54 emergence of replichore size imbalance (9, 10). Recent studies indicate that gene order within 55 the chromosome may play a relevant role in harmonizing the genome structure with cell 56 physiology. Remarkably, key genes coding for nucleoid associated proteins, RNA polymerase 57 modulators, topoisomerases and energy production are arranged along the ori-ter axis following 58 the temporal order of their expression during growth phases (11, 12). In addition, recent studies 59 have showcased an increasing number of traits whose expressio...

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“…In line with this, analysis of the fast-growing bacterium Vibrio cholerae shows that localization of ribosomal genes close to oriC is important for vitality (103,104). Relocating this ribosomal gene cluster to an oriC-distal position resulted in significant growth rate reductions (up to 20%) (103,105). The reduction of growth rate was largest during exponential growth, indicating the gene dosage of these genes does indeed contribute to overexpression.…”

“…In this way, the expression of these growth-related genes is relatively high due to the gene dosage effect during fast growth (98). In line with this, analysis of the fast-growing bacterium Vibrio cholerae shows that localization of ribosomal genes close to oriC is important for vitality (103,104). Relocating this ribosomal gene cluster to an oriC-distal position resulted in significant growth rate reductions (up to 20%) (103,105).…”

“…The reduction of growth rate was largest during exponential growth, indicating the gene dosage of these genes does indeed contribute to overexpression. Addition of a second copy of the gene cluster at the oriC distal position released the growth defect (103).…”