Gammaproteobacterial RNase E-centered RNA degradation

Reusable gammaproteobacterial RNA-degradation module in which the membrane-associated endoribonuclease RNase E initiates decay by 5'-end- dependent internal cleavage and its disordered C-terminal scaffold recruits a DEAD-box helicase and a processive 3'-to-5' exoribonuclease. The helicase unwinds structured decay intermediates so that the exonuclease can complete degradation. The canonical Escherichia coli degradosome uses RhlB and the phosphorolytic PNPase; RhlE and the hydrolytic RNase R are alternative partners in Pseudomonas, so helicase and exonuclease identity are modeled as lineage-variable implementations.

The boundary is RNase E-mediated cleavage plus conditional helicase-assisted and exonuclease-mediated RNA decay. It does not reproduce the broad KEGG bucket: RppH priming, PAP I, Hfq regulation, polyphosphate metabolism, chaperones, RecQ, Rho, and ribosome-biogenesis machinery are adjacent but outside this module. Enolase is excluded because its physical association has not been established for the PSEPK realization and it contributes no catalytic step to decay. The scope is Gammaproteobacteria: RNase E with a partner-recruiting C-terminal scaffold is the shared organizing principle there, while partner composition differs further afield and Firmicutes degrade RNA through RNase Y/J instead of RNase E, so a broader taxon would not share this decomposition. E. coli K-12 and P. putida KT2440 are the exemplars; every grounded protein has a complete gene review. The helicase part is optional because not every substrate requires unwinding. E. coli RhlE is primarily a ribosome-assembly helicase and replaces RhlB only in reconstitution; it is the characterised RhlE-subfamily exemplar for the Pseudomonas RhlE-containing variant, not a claim that E. coli RhlE is a degradosome subunit in vivo. Likewise E. coli RNase R acts in mRNA decay but is not a stable degradosome subunit. The P. putida RhlE and RNase R exemplars are also unproven as RNase E partners: their recruitment into a KT2440 RNase E complex has not been demonstrated, so neither listed representative of the RhlE or RNase R variant is an in vivo case. The only native RNase E-RhlE-RNase R complex, co-purified from cells, is from Pseudomonas syringae Lz4W (PMID:15705581, cited as variant evidence; NCBI taxon 1206777, now Pseudomonas sp. Lz4W). That strain has no UniProtKB entries, so its proteins cannot be added as representative members. Family descriptors use InterPro entries (IPR028878, IPR023554, IPR028622, IPR012162, IPR011805) rather than PANTHER: the member PANTHER families (PTHR30001, PTHR47959, PTHR11252, PTHR23355) are reviewed, but their subfamilies do not isolate the degradosome forms (PTHR30001:SF1 includes a plastid RNE and SF0 mixes RNase G with non-gamma RNase E; PTHR47959:SF13 mixes RhlE with eukaryotic gemin3, MRH4 and DDX31; PTHR23355:SF9 groups RNase R with eukaryotic DIS3L2). PNPase is annotated with polyribonucleotide nucleotidyltransferase activity rather than GO:0000175, which GO places under hydrolytic exonuclease activity. Connections describe functional flow rather than an obligatory sequence for every substrate. Molecular functions are asserted only on leaf annotons.