RNY_BACSU
ID RNY_BACSU Reviewed; 520 AA.
AC O31774;
DT 27-APR-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=Ribonuclease Y;
DE Short=RNase Y;
DE EC=3.1.-.-;
GN Name=rny; Synonyms=ymdA; OrderedLocusNames=BSU16960;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [2]
RP FUNCTION, COFACTOR, ACTIVITY REGULATION, DISRUPTION PHENOTYPE, AND
RP MUTAGENESIS OF HIS-368 AND ASP-369.
RC STRAIN=168 / BGSC1A2;
RX PubMed=19779461; DOI=10.1038/emboj.2009.283;
RA Shahbabian K., Jamalli A., Zig L., Putzer H.;
RT "RNase Y, a novel endoribonuclease, initiates riboswitch turnover in
RT Bacillus subtilis.";
RL EMBO J. 28:3523-3533(2009).
RN [3]
RP FUNCTION IN MRNA-PROCESSING, SUBUNIT, AND DISRUPTION PHENOTYPE.
RC STRAIN=168;
RX PubMed=19193632; DOI=10.1074/mcp.m800546-mcp200;
RA Commichau F.M., Rothe F.M., Herzberg C., Wagner E., Hellwig D.,
RA Lehnik-Habrink M., Hammer E., Volker U., Stulke J.;
RT "Novel activities of glycolytic enzymes in Bacillus subtilis: interactions
RT with essential proteins involved in mRNA processing.";
RL Mol. Cell. Proteomics 8:1350-1360(2009).
RN [4]
RP FUNCTION.
RC STRAIN=BG1;
RX PubMed=20418391; DOI=10.1128/jb.00230-10;
RA Yao S., Bechhofer D.H.;
RT "Initiation of decay of Bacillus subtilis rpsO mRNA by endoribonuclease
RT RNase Y.";
RL J. Bacteriol. 192:3279-3286(2010).
RN [5]
RP INTERACTION WITH CSHA, SUBUNIT, AND SUBCELLULAR LOCATION.
RC STRAIN=168;
RX PubMed=20572937; DOI=10.1111/j.1365-2958.2010.07264.x;
RA Lehnik-Habrink M., Pfortner H., Rempeters L., Pietack N., Herzberg C.,
RA Stulke J.;
RT "The RNA degradosome in Bacillus subtilis: identification of CshA as the
RT major RNA helicase in the multiprotein complex.";
RL Mol. Microbiol. 77:958-971(2010).
RN [6]
RP INTERACTION WITH CSHA; ENO; PFKA; PNP; RNJA AND RNJB, SUBUNIT, AND DOMAIN.
RC STRAIN=168;
RX PubMed=21803996; DOI=10.1128/jb.05500-11;
RA Lehnik-Habrink M., Newman J., Rothe F.M., Solovyova A.S., Rodrigues C.,
RA Herzberg C., Commichau F.M., Lewis R.J., Stulke J.;
RT "RNase Y in Bacillus subtilis: a natively disordered protein that is the
RT functional equivalent of RNase E from Escherichia coli.";
RL J. Bacteriol. 193:5431-5441(2011).
RN [7]
RP INTERACTION WITH DYNA, SUBUNIT, AND SUBCELLULAR LOCATION.
RC STRAIN=168;
RX PubMed=23060960; DOI=10.4161/cib.20215;
RA Buermann F., Sawant P., Bramkamp M.;
RT "Identification of interaction partners of the dynamin-like protein DynA
RT from Bacillus subtilis.";
RL Commun. Integr. Biol. 5:362-369(2012).
RN [8]
RP INTERACTION WITH ENO AND PNP, AND SUBUNIT.
RC STRAIN=168;
RX PubMed=22198292; DOI=10.1016/j.jmb.2011.12.024;
RA Newman J.A., Hewitt L., Rodrigues C., Solovyova A.S., Harwood C.R.,
RA Lewis R.J.;
RT "Dissection of the network of interactions that links RNA processing with
RT glycolysis in the Bacillus subtilis degradosome.";
RL J. Mol. Biol. 416:121-136(2012).
RN [9]
RP FUNCTION IN TYPE I TOXIN-ANTITOXIN BSRG/SR4 DEGRADATION, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=168 / DB104;
RX PubMed=22229825; DOI=10.1111/j.1365-2958.2011.07952.x;
RA Jahn N., Preis H., Wiedemann C., Brantl S.;
RT "BsrG/SR4 from Bacillus subtilis--the first temperature-dependent type I
RT toxin-antitoxin system.";
RL Mol. Microbiol. 83:579-598(2012).
RN [10]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=168;
RX PubMed=22412379; DOI=10.1371/journal.pgen.1002520;
RA Durand S., Gilet L., Bessieres P., Nicolas P., Condon C.;
RT "Three essential ribonucleases-RNase Y, J1, and III-control the abundance
RT of a majority of Bacillus subtilis mRNAs.";
RL PLoS Genet. 8:E1002520-E1002520(2012).
RN [11]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=168 / JH642, 168 / PY79, 168 / W168, and 168 trpC2;
RX PubMed=23504012; DOI=10.1128/jb.00164-13;
RA Figaro S., Durand S., Gilet L., Cayet N., Sachse M., Condon C.;
RT "Bacillus subtilis mutants with knockouts of the genes encoding
RT ribonucleases RNase Y and RNase J1 are viable, with major defects in cell
RT morphology, sporulation, and competence.";
RL J. Bacteriol. 195:2340-2348(2013).
RN [12]
RP FUNCTION IN TYPE I TOXIN-ANTITOXIN BSRE/SR5 DEGRADATION, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=168 / DB104;
RX PubMed=26940229; DOI=10.1080/15476286.2016.1156288;
RA Mueller P., Jahn N., Ring C., Maiwald C., Neubert R., Meissner C.,
RA Brantl S.;
RT "A multistress responsive type I toxin-antitoxin system: bsrE/SR5 from the
RT B. subtilis chromosome.";
RL RNA Biol. 13:511-523(2016).
CC -!- FUNCTION: Endoribonuclease that initiates mRNA decay. Initiates the
CC decay of all SAM-dependent riboswitches, such as yitJ riboswitch.
CC Involved in processing of the gapA operon mRNA, it cleaves between cggR
CC and gapA (PubMed:19193632). Is also the decay-initiating endonuclease
CC for rpsO mRNA. Involved in degradation of type I toxin-antitoxin system
CC bsrG/SR4 RNAs and a minor role in degradation of type I toxin-antitoxin
CC system bsrE/SR5 degradation (PubMed:22229825, PubMed:26940229).
CC {ECO:0000269|PubMed:19193632, ECO:0000269|PubMed:19779461,
CC ECO:0000269|PubMed:20418391, ECO:0000269|PubMed:22229825,
CC ECO:0000269|PubMed:22412379, ECO:0000269|PubMed:23504012,
CC ECO:0000269|PubMed:26940229}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:19779461};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:19779461};
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:19779461};
CC Note=Magnesium. Can also use manganese or zinc.
CC {ECO:0000269|PubMed:19779461};
CC -!- ACTIVITY REGULATION: Shows preference for transcripts carrying a
CC monophosphate group at the 5' end. {ECO:0000269|PubMed:19779461}.
CC -!- SUBUNIT: Homodimer (Probable). Component of a possible RNA degradosome
CC complex composed of rny, rnjA, rnjB, pnp, pfkA and eno
CC (PubMed:19193632) (although rnjA and rnjB's presence is unclear).
CC Interacts with RNA helicase CshA which may also be a member of the RNA
CC degradosome complex (PubMed:20572937). Interacts with full-length
CC dynamin-like protein DynA (PubMed:23060960).
CC {ECO:0000269|PubMed:19193632, ECO:0000269|PubMed:20572937,
CC ECO:0000269|PubMed:21803996, ECO:0000269|PubMed:22198292,
CC ECO:0000269|PubMed:23060960, ECO:0000305}.
CC -!- INTERACTION:
CC O31774; P96614: cshA; NbExp=2; IntAct=EBI-6415578, EBI-6415210;
CC O31774; P37869: eno; NbExp=2; IntAct=EBI-6415578, EBI-6415666;
CC O31774; O34529: pfkA; NbExp=2; IntAct=EBI-6415578, EBI-5250040;
CC O31774; P50849: pnp; NbExp=2; IntAct=EBI-6415578, EBI-5254714;
CC O31774; Q45493: rnjA; NbExp=2; IntAct=EBI-6415578, EBI-6415229;
CC O31774; O31774: rny; NbExp=4; IntAct=EBI-6415578, EBI-6415578;
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000269|PubMed:20572937};
CC Single-pass membrane protein {ECO:0000269|PubMed:20572937}.
CC Note=Dispersed along membrane with a few foci at septation sites and
CC cell poles; in the absence of dynA fewer foci are seen, in the absence
CC of minJ no foci are seen. {ECO:0000269|PubMed:23060960}.
CC -!- DOMAIN: Has 5 domains: N-terminal transmembrane, coiled-coil, KH, HD
CC and an unnamed conserved C-terminal domain (residues 430-520). Both the
CC N-terminal transmembrane helix and C-terminal domain are required for
CC protein function in vivo. {ECO:0000269|PubMed:21803996}.
CC -!- DISRUPTION PHENOTYPE: Essential; depletion mutants show a significant
CC increase in global mRNA half-life (PubMed:19779461) a decrease in at
CC least 1 specific mRNA processing event (PubMed:19193632); in a more
CC severe depletion experiment alteration of about 26% of transcripts was
CC seen (PubMed:22412379). Later shown not to be essential in 4 strains,
CC with a doubled doubling time, cells are translucent, suggesting a
CC possible cell surface defect. 168 trpC2 cells able to grow on minimal
CC medium. Loss of competence for plasmid transformation, 1000-fold less
CC sporulation. Increased sensitivity to a wide range of antibiotics.
CC Thinner cells form long curved structures of 2-3 cell lengths, cell
CC walls are altered with looser, considerably less dense peptidoglycan.
CC Double pnp-rny mutants grow very slowly, while rnjA-rny mutants could
CC not be isolated (PubMed:23504012). Increased half-life of type I toxin-
CC antitoxin system RNAs of BsrG/SR4 (PubMed:22229825).
CC {ECO:0000269|PubMed:19193632, ECO:0000269|PubMed:19779461,
CC ECO:0000269|PubMed:22229825, ECO:0000269|PubMed:22412379,
CC ECO:0000269|PubMed:23504012}.
CC -!- SIMILARITY: Belongs to the RNase Y family. {ECO:0000305}.
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DR EMBL; AL009126; CAB13569.1; -; Genomic_DNA.
DR PIR; F69884; F69884.
DR RefSeq; NP_389578.1; NC_000964.3.
DR RefSeq; WP_003221010.1; NZ_JNCM01000035.1.
DR PDB; 6F7T; X-ray; 2.60 A; C/D=79-90.
DR PDBsum; 6F7T; -.
DR AlphaFoldDB; O31774; -.
DR SMR; O31774; -.
DR IntAct; O31774; 6.
DR STRING; 224308.BSU16960; -.
DR PaxDb; O31774; -.
DR PRIDE; O31774; -.
DR ABCD; O31774; 1 sequenced antibody.
DR DNASU; 939680; -.
DR EnsemblBacteria; CAB13569; CAB13569; BSU_16960.
DR GeneID; 64303587; -.
DR GeneID; 939680; -.
DR KEGG; bsu:BSU16960; -.
DR PATRIC; fig|224308.179.peg.1837; -.
DR eggNOG; COG1418; Bacteria.
DR InParanoid; O31774; -.
DR OMA; PHAILGM; -.
DR PhylomeDB; O31774; -.
DR BioCyc; BSUB:BSU16960-MON; -.
DR SABIO-RK; O31774; -.
DR PRO; PR:O31774; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0004521; F:endoribonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006402; P:mRNA catabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR CDD; cd00077; HDc; 1.
DR Gene3D; 3.30.1370.10; -; 1.
DR HAMAP; MF_00335; RNase_Y; 1.
DR InterPro; IPR003607; HD/PDEase_dom.
DR InterPro; IPR006674; HD_domain.
DR InterPro; IPR006675; HDIG_dom.
DR InterPro; IPR004087; KH_dom.
DR InterPro; IPR004088; KH_dom_type_1.
DR InterPro; IPR036612; KH_dom_type_1_sf.
DR InterPro; IPR017705; Ribonuclease_Y.
DR InterPro; IPR022711; RNase_Y_N.
DR PANTHER; PTHR12826:SF15; PTHR12826:SF15; 1.
DR Pfam; PF01966; HD; 1.
DR Pfam; PF00013; KH_1; 1.
DR Pfam; PF12072; RNase_Y_N; 1.
DR SMART; SM00471; HDc; 1.
DR SMART; SM00322; KH; 1.
DR SUPFAM; SSF54791; SSF54791; 1.
DR TIGRFAMs; TIGR00277; HDIG; 1.
DR TIGRFAMs; TIGR03319; RNase_Y; 1.
DR PROSITE; PS51831; HD; 1.
DR PROSITE; PS50084; KH_TYPE_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell membrane; Coiled coil; Endonuclease; Hydrolase;
KW Membrane; mRNA processing; Nuclease; Reference proteome; RNA-binding;
KW Transmembrane; Transmembrane helix.
FT CHAIN 1..520
FT /note="Ribonuclease Y"
FT /id="PRO_0000163765"
FT TOPO_DOM 1..3
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 4..24
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 25..520
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT DOMAIN 210..273
FT /note="KH"
FT DOMAIN 336..429
FT /note="HD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01175"
FT COILED 29..141
FT /evidence="ECO:0000255"
FT MUTAGEN 1..26
FT /note="MTPIMMVLISILLILLGLVVGYFVRK->MEFVIGLLIVLLALFAAGYFF:
FT Increased protein expression (replaces with transmembrane
FT helix from EzrA)."
FT MUTAGEN 368
FT /note="H->A: Impairs cleavage of the yitJ riboswitch."
FT /evidence="ECO:0000269|PubMed:19779461"
FT MUTAGEN 369
FT /note="D->A: Impairs cleavage of the yitJ riboswitch."
FT /evidence="ECO:0000269|PubMed:19779461"
SQ SEQUENCE 520 AA; 58919 MW; C137937C7665C58C CRC64;
MTPIMMVLIS ILLILLGLVV GYFVRKTIAE AKIAGARGAA EQILEDAKRD AEALKKEALL
EAKDEIHKLR IDAEQEVRER RNELQKQENR LLQKEENLDR KHEGIDKREA MLEKKDHSLN
ERQQHIEEME SKVDEMIRMQ QSELERISSL TRDEAKQIIL ERVENELSHD IAIMTKETEN
RAKEEADKKA KNILSLALQR CAADHVAETT VSVVNLPNDE MKGRIIGREG RNIRTLETLT
GIDLIIDDTP EAVILSGFDP IRRETARIAL DKLVQDGRIH PARIEEMVEK SRREVDDYIR
EMGEQTTFEV GVHGLHPDLI KILGRLKFRT SYGQNVLKHS MEVAFLAGLM ASELGEDAKL
AKRAGLLHDI GKAIDHEVEG SHVEIGVELA TKYKEHPVVI NSIASHHGDE EPTSIIAVLV
AAADALSAAR PGARSETLEN YIRRLEKLEE ISESYEGVEK SFAIQAGREV RIMVKPDSIN
DLEAHRLARD IRKRIEDELD YPGHIKVTVI RETRAVEYAK
