{"doi":"10.1128/jb.00500-08","title":"RNase Activity of Polynucleotide Phosphorylase Is Critical at Low Temperature in<i>Escherichia coli</i>and Is Complemented by RNase II","abstract":"<jats:title>ABSTRACT</jats:title><jats:p>In<jats:italic>Escherichia coli</jats:italic>, the cold shock response is exerted upon a temperature change from 37°C to 15°C and is characterized by induction of several cold shock proteins, including polynucleotide phosphorylase (PNPase), during acclimation phase. In<jats:italic>E. coli</jats:italic>, PNPase is essential for growth at low temperatures; however, its exact role in this essential function has not been fully elucidated. PNPase is a 3′-to-5′ exoribonuclease and promotes the processive degradation of RNA. Our screening of an<jats:italic>E. coli</jats:italic>genomic library for an in vivo counterpart of PNPase that can compensate for its absence at low temperature revealed only one protein, another 3′-to-5′ exonuclease, RNase II. Here we show that the RNase PH domains 1 and 2 of PNPase are important for its cold shock function, suggesting that the RNase activity of PNPase is critical for its essential function at low temperature. We also show that its polymerization activity is dispensable in its cold shock function. Interestingly, the third 3′-to-5′ processing exoribonuclease, RNase R of<jats:italic>E. coli</jats:italic>, which is cold inducible, cannot complement the cold shock function of PNPase. We further show that this difference is due to the different targets of these enzymes and stabilization of some of the PNPase-sensitive mRNAs, like<jats:italic>fis</jats:italic>, in the Δ<jats:italic>pnp</jats:italic>cells has consequences, such as accumulation of ribosomal subunits in the Δ<jats:italic>pnp</jats:italic>cells, which may play a role in the cold sensitivity of this strain.</jats:p>","journal":"Journal of Bacteriology","year":2008,"id":688709,"datarank":0.5897738449086489,"base_score":3.9318256327243257,"endowment":3.9318256327243257,"self_citation_contribution":0.5897738449086489,"citation_network_contribution":0.0,"self_endowment_contribution":0.5897738449086489,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":50,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":138794,"name":"Masayori Inouye","orcid":null,"position":1,"is_corresponding":false},{"id":1797743,"name":"Sangita Phadtare","orcid":null,"position":2,"is_corresponding":false},{"id":1797741,"name":"Naoki Awano","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"RNase Activity of Polynucleotide Phosphorylase Is Critical at Low Temperature in<i>Escherichia coli</i>and Is Complemented by RNase II","abstract":"<jats:title>ABSTRACT</jats:title><jats:p>In<jats:italic>Escherichia coli</jats:italic>, the cold shock response is exerted upon a temperature change from 37°C to 15°C and is characterized by induction of several cold shock proteins, including polynucleotide phosphorylase (PNPase), during acclimation phase. In<jats:italic>E. coli</jats:italic>, PNPase is essential for growth at low temperatures; however, its exact role in this essential function has not been fully elucidated. PNPase is a 3′-to-5′ exoribonuclease and promotes the processive degradation of RNA. Our screening of an<jats:italic>E. coli</jats:italic>genomic library for an in vivo counterpart of PNPase that can compensate for its absence at low temperature revealed only one protein, another 3′-to-5′ exonuclease, RNase II. Here we show that the RNase PH domains 1 and 2 of PNPase are important for its cold shock function, suggesting that the RNase activity of PNPase is critical for its essential function at low temperature. We also show that its polymerization activity is dispensable in its cold shock function. Interestingly, the third 3′-to-5′ processing exoribonuclease, RNase R of<jats:italic>E. coli</jats:italic>, which is cold inducible, cannot complement the cold shock function of PNPase. We further show that this difference is due to the different targets of these enzymes and stabilization of some of the PNPase-sensitive mRNAs, like<jats:italic>fis</jats:italic>, in the Δ<jats:italic>pnp</jats:italic>cells has consequences, such as accumulation of ribosomal subunits in the Δ<jats:italic>pnp</jats:italic>cells, which may play a role in the cold sensitivity of this strain.</jats:p>","is_dataset_classified":null,"base_score":3.9318256327243257,"endowment":3.9318256327243257,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"18606734","pmcid":null,"openalex_id":"https://openalex.org/W2144519149","authors":[],"funders":[],"total_grants":0,"fwci":1.8059,"citation_percentile":0.84795791,"influential_citations":0,"citation_trend":[{"year":2012,"count":5},{"year":2013,"count":4},{"year":2014,"count":3},{"year":2016,"count":4},{"year":2017,"count":2},{"year":2018,"count":2},{"year":2019,"count":1},{"year":2020,"count":2},{"year":2021,"count":1},{"year":2022,"count":3},{"year":2023,"count":4},{"year":2024,"count":4},{"year":2026,"count":2}],"oa_status":"green","license":"https://journals.asm.org/non-commercial-tdm-license","oa_locations":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2519524","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2519524","host_type":"repository"},{"url":"https://journals.asm.org/doi/pdf/10.1128/JB.00500-08","host_type":"publisher"},{"url":"https://doi.org/10.1128/jb.00500-08","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/18606734","host_type":"repository"}],"fields_of_study":["RNA and protein synthesis mechanisms","Bacterial Genetics and Biotechnology","Protein Structure and Dynamics"],"mesh_terms":["Binding Sites","Escherichia coli","Exoribonucleases","Genetic Complementation Test","Mutation","Polyribonucleotide Nucleotidyltransferase","Polyribosomes","Substrate Specificity","Temperature","Gene Expression Regulation, Bacterial","Mutagenesis, Site-Directed","Genome, Bacterial","Dimerization","Escherichia coli Proteins","Ribosome Subunits, Small, Bacterial","Ribosome Subunits, Large, Bacterial"],"keywords":["Polynucleotide phosphorylase","Exoribonuclease","Cold-shock domain","Purine nucleoside phosphorylase","Biology","RNase P","Escherichia coli","RNase PH","Cold sensitivity","Biochemistry","RNase MRP","RNA","Molecular biology","Enzyme","Gene","Mutant"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-19T18:38:55.052349Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}