4.8 Article

Connecting sequence features within the disordered C-terminal linker of Bacillus subtilis FtsZ to functions and bacterial cell division

出版社

NATL ACAD SCIENCES
DOI: 10.1073/pnas.2211178119

关键词

intrinsically disordered proteins; autoregulation; autoinhibition; polymerization; covariation

资金

  1. Washington University Center for Cellular Imaging
  2. Washington University School of Medicine, The Children's Discovery Institute of Washington University
  3. St. Louis Children's Hospital [CDI-CORE-2015-505, CDI-CORE-2019-813]
  4. Foundation for Barnes-Jewish Hospital [FA955020-1-0241]
  5. Air Force Office of Scientific Research [MCB1614766]
  6. NSF [5R35GM127331]
  7. NIH

向作者/读者索取更多资源

Intrinsically disordered regions (IDRs) play a role in autoregulating folded enzymes. The C-terminal tail (CTT) of bacterial cell division protein FtsZ, which includes a disordered C-terminal linker (CTL) and a well-conserved C-terminal peptide (CT17), has been found to make contacts with the T7 loop. Nonrandom sequence patterns within the CTL mediate CTT-core interactions and modulate FtsZ functionalities.
Intrinsically disordered regions (IDRs) can function as autoregulators of folded enzymes to which they are tethered. One example is the bacterial cell division protein FtsZ. This includes a folded core and a C-terminal tail (CTT) that encompasses a poorly conserved, disordered C-terminal linker (CTL) and a well-conserved 17-residue C-terminal peptide (CT17). Sites for GTPase activity of FtsZs are formed at the interface between GTP binding sites and T7 loops on cores of adjacent subunits within dimers. Here, we explore the basis of autoregulatory functions of the CTT in Bacillus subtilis FtsZ (Bs-FtsZ). Molecular simulations show that the CT17 of Bs-FtsZ makes statistically significant CTL-mediated contacts with the T7 loop. Statistical coupling analysis of more than 1,000 sequences from FtsZ orthologs reveals clear covariation of the T7 loop and the CT17 with most of the core domain, whereas the CTL is under independent selection. Despite this, we discover the conservation of nonrandom sequence patterns within CTLs across orthologs. To test how the nonrandom patterns of CTLs mediate CTT-core interactions and modulate FtsZ functionalities, we designed Bs-FtsZ variants by altering the patterning of oppositely charged residues within the CTL. Such alterations disrupt the core-CTT interactions, lead to anomalous assembly and inefficient GTP hydrolysis in vitro and protein degradation, aberrant assembly, and disruption of cell division in vivo. Our findings suggest that viable CTLs in FtsZs are likely to be IDRs that encompass nonrandom, functionally relevant sequence patterns that also preserve three-way covariation of the CT17, the T7 loop, and core domain.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.8
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Article Chemistry, Multidisciplinary

Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains

Anne Bremer, Mina Farag, Wade M. Borcherds, Ivan Peran, Erik W. Martin, Rohit Pappu, Tanja Mittag

Summary: This study uncovers how evolutionarily conserved compositional biases influence the phase behavior of Prion-like low-complexity domains (PLCDs). Tyrosine is identified as a stronger sticker, while lysine weakens sticker-sticker interactions. Additionally, glycine and serine residues act as non-equivalent spacers, impacting the driving forces for phase separation in PLCDs.

NATURE CHEMISTRY (2022)

Article Multidisciplinary Sciences

Dilute phase oligomerization can oppose phase separation and modulate material properties of a ribonucleoprotein condensate

Ian Seim, Ammon E. Posey, Wilton T. Snead, Benjamin M. Stormo, Daphne Klotsa, Rohit Pappu, Amy S. Gladfelter

Summary: This study reveals a mechanism that influences the composition of ribonucleoprotein bodies, in which specific sequence motifs and synergies with the intrinsically disordered region drive the formation of oligomers in the dilute phase, hindering its incorporation into the dense phase. This finding provides new insights for designing synthetic ribonucleoprotein bodies.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Multidisciplinary Sciences

Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically

Xiangze Zeng, Kiersten M. Ruff, Rohit Pappu

Summary: Polyampholytes are the most common type of intrinsically disordered proteins (IDPs), characterized by low net charge and high fractions of charged residues. Recent experiments have revealed differences in conformational preferences for different sequences of polyampholytic IDPs, as well as the existence of various conformations including globules and self-avoiding walks. Atomistic simulations have shown that these IDPs generally sample two stable states, with globules favored by electrostatic attractions and self-avoiding walks favored by favorable hydration energies. The temperature at which these states coexist depends on the sequence, with arginine-rich sequences preferring globular conformations and lysine-rich sequences preferring self-avoiding walks. The length of the side chain also affects the conformational preferences, with shorter side chains favoring necklace-like conformations. Overall, these findings provide insights into the relationship between sequence and conformation in polyampholytic IDPs.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Review Cell Biology

Nutrient availability as an arbiter of cell size

Douglas R. Kellogg, Petra Anne Levin

Summary: Pioneering work discovered that bacterial cell size is proportional to growth rate set by nutrient availability, known as the growth law. Recent studies have shown that the relationship between growth rate, nutrients, and cell size is more complex than originally thought.

TRENDS IN CELL BIOLOGY (2022)

Article Multidisciplinary Sciences

Mesoscale structure-function relationships in mitochondrial transcriptional condensates

Marina Feric, Azadeh Sarfallah, Furqan Dar, Dmitry Temiakov, Rohit Pappu, Tom Misteli

Summary: In live cells, phase separation can organize macromolecules into membraneless structures called biomolecular condensates. Through in vitro experiments, it has been found that mitochondrial components can form multiphasic, viscoelastic condensates, and the transcriptional rates mediated by condensates are lower than in solution, which is associated with the formation of vesicle-like structures driven by the production and accumulation of RNA during transcription.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Chemistry, Physical

Uncovering the Contributions of Charge Regulation to the Stability of Single Alpha Helices

Martin J. Fossat, Ammon E. Posey, Rohit V. Pappu

Summary: The single alpha helix (SAH) is a recurring motif in biology. The sequence with consensus E4K4 repeats shows insensitivity to pH, and the preference for uncharged glutamate residues in internal positions of SAH-forming sequences contributes to this insensitivity. The stability of alpha helical conformations increases with the number of E4K4 repeats, allowing for a larger range of charge states that are compatible with high helical content.

CHEMPHYSCHEM (2023)

Article Biophysics

FIREBALL: A tool to fit protein phase diagrams based on mean-field theories for polymer solutions

Mina Farag, Alex S. Holehouse, Xiangze Zeng, Rohit V. Pappu

Summary: Biomolecular condensates form through phase transitions of biomacromolecules specific to the condensates. Intrinsically disordered regions with appropriate sequence grammars can contribute to the driving forces for phase separation of multivalent proteins through homotypic and heterotypic interactions. Experiments and computations have advanced to the point where the concentrations of coexisting dense and dilute phases can be measured or computed for individual intrinsically disordered regions. The development of computational tools like FIREBALL enables efficient analysis and fitting of experimental or computed data of binodals, providing insight into the coil-to-globule transitions of macromolecules.

BIOPHYSICAL JOURNAL (2023)

Review Chemistry, Multidisciplinary

Phase Transitions of Associative Biomacromolecules

Rohit Pappu, Samuel R. Cohen, Furqan Dar, Mina Farag, Mrityunjoy Kar

Summary: In this review, we discuss the role of multivalent associative biomacromolecules, such as proteins and nucleic acids, in the formation and regulation of biomolecular condensates. We also explore the concepts of phase transitions in aqueous solutions of these associative biomacromolecules and their relevance to biomolecular condensates.

CHEMICAL REVIEWS (2023)

Article Biochemistry & Molecular Biology

Developments in describing equilibrium phase transitions of multivalent associative macromolecules

Xiangze Zeng, Rohit V. Pappu

Summary: Biomolecular condensates are specific cellular structures that can organize cellular matter and biochemical reactions in space and time. They are formed and dissolved through spontaneous and driven phase transitions of multivalent associative macromolecules. Current progress has focused on modeling sequence-specific phase transitions, especially for intrinsically disordered proteins. In this review, we summarize the state-of-the-art theories and computations aimed at understanding and modeling sequence-specific, thermodynamically controlled, coupled associative and segregative phase transitions of archetypal multivalent macromolecules.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2023)

Article Chemistry, Physical

SOURSOP: A Python Package for the Analysis of Simulations of Intrinsically Disordered Proteins

Jared M. Lalmansingh, Alex T. Keeley, Kiersten M. Ruff, Rohit V. Pappu, Alex S. Holehouse

Summary: Conformational heterogeneity is a characteristic feature of intrinsically disordered proteins and protein regions. Simulations based on atomistic and coarse-grained models are commonly used to understand the sequence-specific interactions and functions of these proteins. In this study, a new analysis toolkit called SOURSOP is introduced, which provides a collection of easy-to-use functions to characterize the conformational ensembles of intrinsically disordered proteins.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2023)

Article Chemistry, Multidisciplinary

RNAs undergo phase transitions with lower critical solution temperatures

Gable M. Wadsworth, Walter J. Zahurancik, Xiangze Zeng, Paul Pullara, Lien B. Lai, Vaishnavi Sidharthan, Rohit V. Pappu, Venkat Gopalan, Priya R. Banerjee

Summary: Co-phase separation of RNAs and RNA-binding proteins is an important driving force for the biogenesis of ribonucleoprotein granules. It has been discovered that RNA can also undergo phase transitions in the absence of proteins, driven by entropy and modulated by RNA bases. The presence of magnesium ions enables RNA-only condensates to also undergo percolation transitions, leading to arrested condensates.

NATURE CHEMISTRY (2023)

Article Multidisciplinary Sciences

Phase separation of protein mixtures is driven by the interplay of homotypic and heterotypic interactions

Mina Farag, Wade M. Borcherds, Anne Bremer, Tanja Mittag, Rohit V. Pappu

Summary: Through simulations and experiments, researchers found that mixtures of RNA-binding proteins' PLCDs undergo phase separation more readily than individual PLCDs due to complementary electrostatic interactions. They revealed how stoichiometric ratios of different components and their sequence-encoded interactions contribute to the driving forces for condensate formation, and how interaction strengths and sequence lengths modulate conformational preferences of molecules at condensates' interfaces.

NATURE COMMUNICATIONS (2023)

暂无数据