Proceedings of the National Academy of Sciences of the United States of America最新文献_第5页

Evolution and evolvability of rifampicin resistance across the bacterial tree of life 细菌生命树中利福平耐药性的进化和进化性

IF 11.1 1区综合性期刊

Proceedings of the National Academy of Sciences of the United States of America Pub Date : 2025-07-30 DOI: 10.1073/pnas.2424307122

Negin Bolourchi, Christopher R. P. Brown, Andrew D. Letten, Jan Engelstädter

{"title":"Evolution and evolvability of rifampicin resistance across the bacterial tree of life","authors":"Negin Bolourchi, Christopher R. P. Brown, Andrew D. Letten, Jan Engelstädter","doi":"10.1073/pnas.2424307122","DOIUrl":"https://doi.org/10.1073/pnas.2424307122","url":null,"abstract":"Predicting the ability of bacteria to develop antibiotic resistance is challenging, especially for the vast majority of species for which no experimental data are available. Here, we investigated the evolvability and intrinsic presence of rifampicin resistance across the bacterial tree of life. We compiled a comprehensive panel of known rifampicin resistance mutations, comprising 57 amino acid substitutions within the gene rpoB . We then screened more than 18,000 genomes from all major bacterial groups for the presence of those mutations and determined which mutations can evolve through point mutations. Our results demonstrate that although the evolvability of individual mutations varies considerably across species, overall predicted evolvability is high and relatively homogeneous across bacterial taxa. Rifampicin resistance mutations are present intrinsically in 8% of species that tend to be phylogenetically clustered. Our analysis provides a global picture of the mutational landscape of rifampicin resistance, affording insight into existing observations and informing future discoveries such as the identification of probiotics.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"26 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144747328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

AI–AI bias: Large language models favor communications generated by large language models AI-AI偏差：大型语言模型倾向于由大型语言模型生成的通信

IF 11.1 1区综合性期刊

Proceedings of the National Academy of Sciences of the United States of America Pub Date : 2025-07-29 DOI: 10.1073/pnas.2415697122

Walter Laurito, Benjamin Davis, Peli Grietzer, Tomáš Gavenčiak, Ada Böhm, Jan Kulveit

引用次数: 0

Phage-based delivery of CRISPR-associated transposases for targeted bacterial editing. 靶向细菌编辑的基于噬菌体的crispr相关转座传递。

IF 9.4 1区综合性期刊

Proceedings of the National Academy of Sciences of the United States of America Pub Date : 2025-07-29 Epub Date: 2025-07-25 DOI: 10.1073/pnas.2504853122

Avery Roberts, Benjamin A Adler, Brady F Cress, Jennifer A Doudna, Rodolphe Barrangou

{"title":"Phage-based delivery of CRISPR-associated transposases for targeted bacterial editing.","authors":"Avery Roberts, Benjamin A Adler, Brady F Cress, Jennifer A Doudna, Rodolphe Barrangou","doi":"10.1073/pnas.2504853122","DOIUrl":"https://doi.org/10.1073/pnas.2504853122","url":null,"abstract":"Phage λ, a well-characterized temperate phage, has been recently leveraged for bacterial genome editing by selectively delivering base editors into targeted bacterial species. We extend this concept by engineering phage λ to deliver CRISPR-guided transposases, accomplishing large insertions and targeted gene disruptions. To achieve this, we engineered phage λ using homologous recombination paired with Cas13a-based counterselection for precise phage modifications. Initially, we established the utility of Cas13a in phage λ by conducting minimal recoding edits, deletions, and insertions. Subsequently, we scaled up the engineering to embed the comprehensive DNA-editing CRISPR-Cas transposase (DART) system within the phage genome, creating λ-DART phages. These modified λ-DART phages were then employed to infect Escherichia coli, generating CRISPR RNA-guided transposition events in the host genome. Applying our engineered λ-DART phages to monocultures and a mixed bacterial community comprising three genera led to efficient, precise, and specific gene knockouts and insertions in the targeted E. coli cells, achieving editing efficiencies surpassing 50% of the population. This research enhances phage-mediated genome editing by enabling efficient in situ gene integrations in bacteria, offering an avenue for further application in microbial community contexts. This scalable method enables flexible microbial genome editing in situ to manipulate the function and composition of diverse ecosystems.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 30","pages":"e2504853122"},"PeriodicalIF":9.4,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144715178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Synthesis of large single-transcript pathways from oligonucleotide pools: Design of STARBURST, an autobioluminescent reporter 从寡核苷酸池中合成大的单转录途径：STARBURST的设计，一个自身生物发光的报告细胞

IF 11.1 1区综合性期刊

Proceedings of the National Academy of Sciences of the United States of America Pub Date : 2025-07-29 DOI: 10.1073/pnas.2508109122

Gony Dvir, Zenan Xing, Irina Beldman, Andrés Rivera, Ian Wheeldon, Sean R. Cutler

{"title":"Synthesis of large single-transcript pathways from oligonucleotide pools: Design of STARBURST, an autobioluminescent reporter","authors":"Gony Dvir, Zenan Xing, Irina Beldman, Andrés Rivera, Ian Wheeldon, Sean R. Cutler","doi":"10.1073/pnas.2508109122","DOIUrl":"https://doi.org/10.1073/pnas.2508109122","url":null,"abstract":"Methods for fast and inexpensive gene synthesis from oligonucleotide pools enable rapid iteration of genetic designs. Here, we describe iggypop (indexed Golden Gate gene assembly from PCR-amplified oligonucleotide pools), a simple computational–experimental pipeline that allows for low-cost design and synthesis of hundreds of genes from oligonucleotide pools using Golden Gate assembly methods. We used iggypop to synthesize a series of single-transcript autonomously bioluminescent reporters (STARBURSTs) that link the five genes of a fungal bioluminescence pathway via ribosomal skipping LP4/2A sequences into a 9.5 kb transcript that function in planta. We also synthesized RUBY reporters (a reporter gene system producing red betalain pigment) recoded to match dicot codon usage, as RUBY was codon optimized for rice codon usage and has a high GC content. Surprisingly, the recoded RUBYs substantially reduced betalain production in transient Nicotiana benthamiana assays. Based on this observation, we synthesized six GC-boosted STARBURSTs, which produced robust luminescence in both transient assays and transgenic Arabidopsis plants. Thus, iggypop enabled the rapid synthesis of multiple genetic designs to deliver a bright single transcript autobioluminescent reporter. Iggypop should enable the facile synthesis and optimization of new genetic parts and complex polycistronic pathways.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"1 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144737046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In This Issue. 在本期中。

IF 9.1 1区综合性期刊

Proceedings of the National Academy of Sciences of the United States of America Pub Date : 2025-07-29 DOI: 10.1073/iti3025122

引用次数: 0

Bivalent interaction through an intrinsically disordered linker promotes transcription activation complex assembly in Notch signaling. 通过内在无序连接子的二价相互作用促进Notch信号的转录激活复合物组装。

IF 9.4 1区综合性期刊

Proceedings of the National Academy of Sciences of the United States of America Pub Date : 2025-07-29 Epub Date: 2025-07-25 DOI: 10.1073/pnas.2501607122

Cyril Cook, Kristen M Ramsey, Doug Barrick

{"title":"Bivalent interaction through an intrinsically disordered linker promotes transcription activation complex assembly in Notch signaling.","authors":"Cyril Cook, Kristen M Ramsey, Doug Barrick","doi":"10.1073/pnas.2501607122","DOIUrl":"https://doi.org/10.1073/pnas.2501607122","url":null,"abstract":"The Notch signaling pathway regulates cellular differentiation by activating transcription through an unusual heterotrimeric complex comprising the Notch receptor's intracellular domain (NICD), the DNA-binding protein CSL, and the coactivator MAML. NICD has two binding sites for CSL, a short motif in the RAM region and an ankyrin domain (ANK), connected by an intrinsically disordered linker and which form a bivalent ternary complex with CSL and MAML. Although bivalency is required for maximal transcription activation, the energetic contributions of bivalency and heterotrimer formation within this essential complex are unknown. To elucidate the energetics of bivalency, we first determine the free energy of the CSL-ANK-MAML heterotrimer, using isothermal titration calorimetry and developing an obligate heterotrimer model to analyze the data. By comparing this heterotrimerization reaction with binding reactions involving different regions of RAMANK, we determine the energetic contribution of bivalency to heterotrimer assembly. We show that bivalency through the disordered linker increases the effective concentration of ANK, and that the bivalent interaction enhances occupancy of RAM and ANK at their binding sites on CSL by about three orders of magnitude. By redefining the standard state to a lower, more physiological protein concentration, we reveal the importance of the RAMANK intrinsically disordered linker for assembly of the Notch transcription activation complex. This work provides a framework whereby the energetic contributions of intrinsically disordered linkers to higher-order multivalent assembly may be analyzed.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 30","pages":"e2501607122"},"PeriodicalIF":9.4,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144715175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Deficiency in transmitter release triggers homeostatic transcriptional changes that increase presynaptic excitability 缺乏递质释放触发稳态转录变化，增加突触前兴奋性

IF 11.1 1区综合性期刊

Proceedings of the National Academy of Sciences of the United States of America Pub Date : 2025-07-29 DOI: 10.1073/pnas.2322714122

Caroline A. Cypranowska, Maya Feldthouse, Yoon Gi Choi, Dariya Bakshinska, Rachel Li, Zachary L. Newman, Ehud Y. Isacoff

引用次数: 0

Structural basis for the evolution of a domesticated group II intron–like reverse transcriptase to function in host cell DNA repair 驯化II组内含子样逆转录酶在宿主细胞DNA修复中的功能进化的结构基础

IF 11.1 1区综合性期刊

Proceedings of the National Academy of Sciences of the United States of America Pub Date : 2025-07-29 DOI: 10.1073/pnas.2504208122

Seung Kuk Park, Mo Guo, Jennifer L. Stamos, Wantae Kim, Sidae Lee, Y. Jessie Zhang, Alan M. Lambowitz

{"title":"Structural basis for the evolution of a domesticated group II intron–like reverse transcriptase to function in host cell DNA repair","authors":"Seung Kuk Park, Mo Guo, Jennifer L. Stamos, Wantae Kim, Sidae Lee, Y. Jessie Zhang, Alan M. Lambowitz","doi":"10.1073/pnas.2504208122","DOIUrl":"https://doi.org/10.1073/pnas.2504208122","url":null,"abstract":"A previous study found that a bacterial group II intron–like reverse transcriptase (G2L4 RT) evolved to function in double-strand break repair (DSBR) via microhomology-mediated end-joining (MMEJ) and that a mobile group II intron-encoded RT has a basal DSBR activity that uses conserved structural features of non-long terminal repeat (non-LTR)-retroelement RTs. Here, we determined G2L4 RT apoenzyme and snap-back DNA synthesis structures revealing unique structural adaptations that optimized its cellular function in DSBR. These included an RT3a structure that stabilizes the apoenzyme in an inactive conformation until encountering a DNA substrate; a longer N-terminal extension/RT0-loop with conserved residues that together with a modified active site favors strand annealing; and a conserved dimer interface that localizes G2L4 RT homodimers to DSBR sites with both monomers positioned for MMEJ. Our findings reveal how an RT can function in DNA repair and suggest ways of optimizing related RTs for genome engineering applications.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"13 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144737043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The kinesin KIF3AC recycles endocytosed integrin to polarize new adhesion formation toward the leading edge. 驱动蛋白KIF3AC循环内吞整合素，使新的粘附形成向前沿极化。

IF 9.1 1区综合性期刊

Proceedings of the National Academy of Sciences of the United States of America Pub Date : 2025-07-29 Epub Date: 2025-07-24 DOI: 10.1073/pnas.2513776122

Johnny A Z Rockenbach, Guilherme P F Nader, Susumu Antoku, Gregg G Gundersen

{"title":"The kinesin KIF3AC recycles endocytosed integrin to polarize new adhesion formation toward the leading edge.","authors":"Johnny A Z Rockenbach, Guilherme P F Nader, Susumu Antoku, Gregg G Gundersen","doi":"10.1073/pnas.2513776122","DOIUrl":"10.1073/pnas.2513776122","url":null,"abstract":"The recycling of integrin endocytosed during focal adhesion (FA) disassembly is critical for cell migration and contributes to the polarized formation of new FAs toward the leading edge. How this occurs is unclear. Here, we sought to identify the kinesin motor protein(s) that is involved in recycling endocytosed integrin back to the plasma membrane. We show that the kinesin-2 heterodimer, KIF3AC, and the Rab11 adaptor protein Rab coupling protein (RCP) are required for FA reformation after the disassembly of FAs in mouse and human fibroblasts. In the absence of KIF3AC, integrin does not return to the cell surface after FA disassembly and is found in the Rab11 endocytic recycling compartment. Biochemical pulldowns revealed that KIF3C associated with β1 integrin in an RCP-dependent fashion, but only after FA disassembly. KIF3AC knockdown inhibited cell migration, trafficking of RCP toward the leading edge, and polarized formation of FAs at the leading edge. These results show that KIF3AC promotes cell migration by recycling integrin so that it generates new FAs in a polarized fashion.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 30","pages":"e2513776122"},"PeriodicalIF":9.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Tensor-based quantum phase difference estimation for large-scale demonstration. 基于张量的大规模论证量子相位差估计。

IF 9.4 1区综合性期刊

Proceedings of the National Academy of Sciences of the United States of America Pub Date : 2025-07-29 Epub Date: 2025-07-24 DOI: 10.1073/pnas.2425026122

Shu Kanno, Kenji Sugisaki, Hajime Nakamura, Hiroshi Yamauchi, Rei Sakuma, Takao Kobayashi, Qi Gao, Naoki Yamamoto

引用次数: 0