Ning Lu

All Publications

• Scaffold-Scaffold Interaction Facilitates Cell Polarity Development in Caulobacter crescentus MBIO Lu, N., Duvall, S. W., Zhao, G., Kowallis, K. A., Zhang, C., Tan, W., Sun, J., Petitjean, H. N., Tomares, D. T., Zhao, G., Childers, W., Zhao, W. 2023: e0321822

  Abstract

  Cell polarity development is the prerequisite for cell differentiation and generating biodiversity. In the model bacterium Caulobacter crescentus, the polarization of the scaffold protein PopZ during the predivisional cell stage plays a central role in asymmetric cell division. However, our understanding of the spatiotemporal regulation of PopZ localization remains incomplete. In the current study, a direct interaction between PopZ and the new pole scaffold PodJ is revealed, which plays a primary role in triggering the new pole accumulation of PopZ. The coiled-coil 4-6 domain in PodJ is responsible for interacting with PopZ in vitro and promoting PopZ transition from monopolar to bipolar in vivo. Elimination of the PodJ-PopZ interaction impairs the PopZ-mediated chromosome segregation by affecting both the positioning and partitioning of the ParB-parS centromere. Further analyses of PodJ and PopZ from other bacterial species indicate this scaffold-scaffold interaction may represent a widespread strategy for spatiotemporal regulation of cell polarity in bacteria. IMPORTANCE Caulobacter crescentus is a well-established bacterial model to study asymmetric cell division for decades. During cell development, the polarization of scaffold protein PopZ from monopolar to bipolar plays a central role in C. crescentus asymmetric cell division. Nevertheless, the spatiotemporal regulation of PopZ has remained unclear. Here, we demonstrate that the new pole scaffold PodJ functions as a regulator in triggering PopZ bipolarization. The primary regulatory role of PodJ was demonstrated in parallel by comparing it with other known PopZ regulators, such as ZitP and TipN. Physical interaction between PopZ and PodJ ensures the timely accumulation of PopZ at the new cell pole and the inheritance of the polarity axis. Disruption of the PodJ-PopZ interaction impaired PopZ-mediated chromosome segregation and may lead to a decoupling of DNA replication from cell division during the cell cycle. Together, the scaffold-scaffold interaction may provide an underlying infrastructure for cell polarity development and asymmetric cell division.

  View details for DOI 10.1128/mbio.03218-22

  View details for Web of Science ID 000952673900001

  View details for PubMedID 36971555

  View details for PubMedCentralID PMC10127582

• Phase separation modulates the assembly and dynamics of a polarity-related scaffold-signaling hub NATURE COMMUNICATIONS Tan, W., Cheng, S., Li, Y., Li, X., Lu, N., Sun, J., Tang, G., Yang, Y., Cai, K., Li, X., Ou, X., Gao, X., Zhao, G., Childers, W., Zhao, W. 2022; 13 (1): 7181

  Abstract

  Asymmetric cell division (ACD) produces morphologically and behaviorally distinct cells and is the primary way to generate cell diversity. In the model bacterium Caulobacter crescentus, the polarization of distinct scaffold-signaling hubs at the swarmer and stalked cell poles constitutes the basis of ACD. However, mechanisms involved in the formation of these hubs remain elusive. Here, we show that a swarmer-cell-pole scaffold, PodJ, forms biomolecular condensates both in vitro and in living cells via phase separation. The coiled-coil 4-6 and the intrinsically disordered regions are the primary domains that contribute to biomolecular condensate generation and signaling protein recruitment in PodJ. Moreover, a negative regulation of PodJ phase separation by the stalked-cell-pole scaffold protein SpmX is revealed. SpmX impedes PodJ cell-pole accumulation and affects its recruitment ability. Together, by modulating the assembly and dynamics of scaffold-signaling hubs, phase separation may serve as a general biophysical mechanism that underlies the regulation of ACD in bacteria and other organisms.

  View details for DOI 10.1038/s41467-022-35000-2

  View details for Web of Science ID 000887967800014

  View details for PubMedID 36418326

  View details for PubMedCentralID PMC9684454

• Cdc13 is predominant over Stn1 and Ten1 in preventing chromosome end fusions ELIFE Wu, Z., Liu, J., Man, X., Gu, X., Li, T., Cai, C., He, M., Shao, Y., Lu, N., Xue, X., Qin, Z., Zhou, J. 2020; 9

  Abstract

  Telomeres define the natural ends of eukaryotic chromosomes and are crucial for chromosomal stability. The budding yeast Cdc13, Stn1 and Ten1 proteins form a heterotrimeric complex, and the inactivation of any of its subunits leads to a uniformly lethal phenotype due to telomere deprotection. Although Cdc13, Stn1 and Ten1 seem to belong to an epistasis group, it remains unclear whether they function differently in telomere protection. Here, we employed the single-linear-chromosome yeast SY14, and surprisingly found that the deletion of CDC13 leads to telomere erosion and intrachromosome end-to-end fusion, which depends on Rad52 but not Yku. Interestingly, the emergence frequency of survivors in the SY14 cdc13Δ mutant was ~29 fold higher than that in either the stn1Δ or ten1Δ mutant, demonstrating a predominant role of Cdc13 in inhibiting telomere fusion. Chromosomal fusion readily occurred in the telomerase-null SY14 strain, further verifying the default role of intact telomeres in inhibiting chromosome fusion.

  View details for DOI 10.7554/eLife.53144

  View details for Web of Science ID 000558756700001

  View details for PubMedID 32755541

  View details for PubMedCentralID PMC7406354

• Creating functional chromosome fusions in yeast with CRISPR-Cas9 NATURE PROTOCOLS Shao, Y., Lu, N., Xue, X., Qin, Z. 2019; 14 (8): 2521-2545

  Abstract

  CRISPR-Cas9-facilitated functional chromosome fusion allows the generation of a series of yeast strains with progressively reduced chromosome numbers that are valuable resources for the study of fundamental concepts in chromosome biology, including replication, recombination and segregation. We created a new yeast strain with a single chromosome by using the protocol for chromosome fusion described herein. To ensure the accuracy of chromosome fusions in yeast, the long redundant repetitive sequences near linear chromosomal ends are deleted, and the fusion orders are correspondingly determined. Possible influence on gene expression is minimized to retain gene functionality. This protocol provides experimentally derived guidelines for the generation of functional chromosome fusions in yeast, especially for the deletion of repetitive sequences, the determination of the fusion order and cleavage sites, and primary evaluation of the functionality of chromosome fusions. Beginning with design, one round of typical chromosome fusion and functional verifications can be accomplished within 18 d.

  View details for DOI 10.1038/s41596-019-0192-0

  View details for Web of Science ID 000477795000010

  View details for PubMedID 31300803

  View details for PubMedCentralID 1209127

• A single circular chromosome yeast CELL RESEARCH Shao, Y., Lu, N., Cai, C., Zhou, F., Wang, S., Zhao, Z., Zhao, G., Zhou, J., Xue, X., Qin, Z. 2019; 29 (1): 87-89

  View details for DOI 10.1038/s41422-018-0110-y

  View details for Web of Science ID 000454806600011

  View details for PubMedID 30559437

  View details for PubMedCentralID PMC6318310

• CRISPR-Cas9 Facilitated Multiple-Chromosome Fusion in Saccharomyces cerevisiae ACS SYNTHETIC BIOLOGY Shao, Y., Lu, N., Qin, Z., Xue, X. 2018; 7 (11): 2706-2708

  Abstract

  Eukaryotic cells usually contain multiple linear chromosomes. Recently, we artificially created a functional single-chromosome yeast via sequential two-chromosome fusion utilizing the high performance of the CRISPR-Cas9 system and homologous recombination in Saccharomyces cerevisiae. In this paper, we adapted this method for the simultaneous fusion of multiple chromosomes. We demonstrated the fusion of two, two-chromosome sets with a 75% positive rate and three-chromosome fusions with a 50% positive rate. We also found that by using an additional selection marker, the positive rate of two-chromosome fusions reached 100%. Due to the simplicity, efficiency, and portability of this method, we expect that it can be easily adapted for multiple-chromosome fusions in other organisms.

  View details for DOI 10.1021/acssynbio.8b00397

  View details for Web of Science ID 000451100900025

  View details for PubMedID 30352154

• Creating a functional single-chromosome yeast NATURE Shao, Y., Lu, N., Wu, Z., Cai, C., Wang, S., Zhang, L., Zhou, F., Xiao, S., Liu, L., Zeng, X., Zheng, H., Yang, C., Zhao, Z., Zhao, G., Zhou, J., Xue, X., Qin, Z. 2018; 560 (7718): 331-+

  Abstract

  Eukaryotic genomes are generally organized in multiple chromosomes. Here we have created a functional single-chromosome yeast from a Saccharomyces cerevisiae haploid cell containing sixteen linear chromosomes, by successive end-to-end chromosome fusions and centromere deletions. The fusion of sixteen native linear chromosomes into a single chromosome results in marked changes to the global three-dimensional structure of the chromosome due to the loss of all centromere-associated inter-chromosomal interactions, most telomere-associated inter-chromosomal interactions and 67.4% of intra-chromosomal interactions. However, the single-chromosome and wild-type yeast cells have nearly identical transcriptome and similar phenome profiles. The giant single chromosome can support cell life, although this strain shows reduced growth across environments, competitiveness, gamete production and viability. This synthetic biology study demonstrates an approach to exploration of eukaryote evolution with respect to chromosome structure and function.

  View details for DOI 10.1038/s41586-018-0382-x

  View details for Web of Science ID 000441673400032

  View details for PubMedID 30069045