Review
Making the Case for Disordered Proteins and Biomolecular Condensates in Bacteria

https://doi.org/10.1016/j.tibs.2020.04.011Get rights and content

Highlights

  • Although bacterial proteomes are deficient in intrinsically disordered regions (IDRs) compared with eukaryotic counterparts, growing evidence shows that IDRs are essential to the functions of several proteins that contribute to all aspects of bacterial lifecycles.

  • As in eukaryotic systems, bacterial IDRs have been shown to contribute to and even drive the formation of biomolecular condensates that control key cellular processes such as division, transcription, post-transcriptional processing, and stress response.

  • In many systems, specifically those highlighted here, IDRs are tethered to folded domains and contribute directly to molecular functions.

  • Borrowing concepts from eukaryotic systems, we can describe the bacterial IDRs that form condensates with a stickers and spacers framework.

  • Key proteins involving IDRs feature either encoded or emergent multivalence of interaction motifs (stickers) that coordinate networks of homotypic and heterotypic interactions.

Intrinsically disordered proteins/regions (IDPs/IDRs) contribute to a diverse array of molecular functions in eukaryotic systems. There is also growing recognition that membraneless biomolecular condensates, many of which are organized or regulated by IDPs/IDRs, can enable spatial and temporal regulation of complex biochemical reactions in eukaryotes. Motivated by these findings, we assess if (and how) membraneless biomolecular condensates and IDPs/IDRs are functionally involved in key cellular processes and molecular functions in bacteria. We summarize the conceptual underpinnings of condensate assembly and leverage these concepts by connecting them to recent findings that implicate specific types of condensates and IDPs/IDRs in important cellular level processes and molecular functions in bacterial systems.

Section snippets

Biochemical Reactions Have to Be Organized in Space and Time

Spatial and temporal regulation of cellular matter is necessary for the control of transcription, protein quality control, cell signaling, and responses to stimuli [1]. In many eukaryotic systems as well as in bacterial systems (the focus of this article), the reversible formation of membraneless biomolecular condensates – referred to hereafter as condensates – provides the necessary spatiotemporal control by organizing biochemical reactions, enabling quality control, and concentrating cellular

Principles Underlying Phase Transitions of Multivalent Macromolecules

Interchain physical crosslinks among stickers enables a networking transition known as bond percolation [10,13., 14., 15.,17,18]. This happens above a system-specific threshold concentration known as the percolation threshold that is designated as cperc. Above cperc, the collection of multivalent macromolecules in solution will form a system-spanning network [11,14,15] (Figure 2). These transitions are also known as sol–gel transitions [26], but we prefer the term bond percolation to avoid

Spatiotemporal Control of Bacterial Division

The initiation of cell division in rod-shaped bacteria is marked by the formation of a cytokinetic ring at the cell center [70]. A family of proteins, termed the divisome, collectively functions to constrict the ring in the center of the cell, synthesize new material, and pinch the cell in two [71]. The bacterial cytokinetic ring is scaffolded by the tubulin homolog FtsZ that serves as a treadmilling interaction hub for many of the adaptor proteins of the divisome [72., 73., 74.]. FtsZ

Spatiotemporal Control of Polarity

Another area of spatial and temporal organization pertains to the regulation of asymmetric division and polarity that has been reported in Caulobacter crescentus. Here, a differentiated stalked cell can enter the cell division cycle and in doing so, it ensures that the cytoplasmic space has two sides: a future swarmer and the old stalk cell [69,92,93]. Polar organizing protein (Pop)Z is 57% disordered and it is a major player in differentiation [92,94,95]. PopZ oligomerizes and forms an

Control of DNA Replication

In bacterial DNA replication and repair, single-stranded DNA binding proteins (SSBs) play an essential role. Their modular architecture, which is reminiscent of FtsZ, includes an ordered DNA-binding domain (OB fold), followed by a hypervariable intrinsically disordered linker (IDL/spacer) that is connected to a conserved C-terminal tip (sticker) [63,64,102]. SSBs oligomerize to form homotetramers that leads to a fourfold increase in the valence of stickers that coordinate interactions with SSB

Control of Transcription

Transcriptional foci in E. coli also involve RNAP and bear the hallmarks of condensates. In slow-growing conditions, RNAP is uniformly dispersed throughout the cell, whereas in fast-growing conditions, RNAP becomes localized to distinct puncta, potentially optimizing ribosomal production [108., 109., 110.] – akin to nucleoli in eukaryotes [38]. Puncta that were previously thought to form via DNA binding were shown to dissolve with the addition of 1′6 hexanediol to the media, indicating that the

Bacterial Condensates in Protein Quality Control

Another process controlled by condensates in bacteria is that of RNA degradation [112., 113., 114.]. In this system, RNaseE is a critical driver of the formation of the RNA degradasome. The architecture of RNaseE includes a conserved DEAD-box RNA helicase and a disordered C-terminal domain (CTD). In C. crescentus, the RNaseE CTD is necessary and sufficient to drive phase separation. In vivo RNaseE drives the formation of cytoplasmic foci that colocalize with other exonucleases. This degradation

Management of Phosphate Levels and Synthesis of Multivalent Phosphates

Bacteria utilize novel mechanisms to manage intracellular phosphate levels, particularly at times of nutrient deprivation. Under these conditions, bacteria will burn ATP to synthesize long polyphosphate (PolyP) chains that coalesce into large granules that are required for survival. These PolyP granules sequester certain proteins including the polyphosphate-synthesizing enzyme Ppk1 [117]. Polyphosphates are reminiscent of nucleic acid backbones and it appears that the physical principles

Concluding Remarks

We have focused on specific examples (Figure 3, Key Figure) to make the case that IDRs and biomolecular condensates have relevant and important roles to play in bacteria. In doing so, we have relied on the minimalist definition provided by Banani et al. [2] for designating membraneless bodies as condensates. Whether these condensates form and dissolve via spontaneous (passive) or driven (active) PSP transitions [54] will need to be resolved via systematic assessments in vitro and in vivo. There

Acknowledgments

This work was supported by grants to R.V.P. from the US National Science Foundation (MCB-1614766) and the Human Frontier Science Program (RGP0034/2017). We are grateful to Alex Holehouse, Keren Lasker, Petra Levin, Timothy Lohman, Kiersten Ruff, and Saumya Saurabh for critical reading of the manuscript and numerous stimulating discussions regarding IDRs in bacteria and their relevance to cellular regulation. R.V.P. acknowledges ongoing and engaging interactions with Simon Alberti, Clifford

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