ID   HPF_BACSU               Reviewed;         189 AA.
AC   P28368;
DT   01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1995, sequence version 2.
DT   03-AUG-2022, entry version 125.
DE   RecName: Full=Ribosome hibernation promotion factor {ECO:0000255|HAMAP-Rule:MF_00839};
DE            Short=HPF {ECO:0000255|HAMAP-Rule:MF_00839};
DE   AltName: Full=Hst23 {ECO:0000303|PubMed:9852014};
DE   AltName: Full=Putative sigma-54 modulation protein;
DE   AltName: Full=SigL modulation protein;
GN   Name=yvyD; Synonyms=hpf {ECO:0000255|HAMAP-Rule:MF_00839}, yviI;
GN   OrderedLocusNames=BSU35310; ORFNames=orf189;
OS   Bacillus subtilis (strain 168).
OC   Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX   NCBI_TaxID=224308;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=168 / HB2058;
RX   PubMed=8195064; DOI=10.1128/jb.176.11.3093-3101.1994;
RA   Chen L., Helmann J.D.;
RT   "The Bacillus subtilis sigma D-dependent operon encoding the flagellar
RT   proteins FliD, FliS, and FliT.";
RL   J. Bacteriol. 176:3093-3101(1994).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=168;
RX   PubMed=8969505; DOI=10.1099/13500872-142-11-3079;
RA   Soldo B., Lazarevic V., Mauel C., Karamata D.;
RT   "Sequence of the 305 degrees-307 degrees region of the Bacillus subtilis
RT   chromosome.";
RL   Microbiology 142:3079-3088(1996).
RN   [3]
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   [4]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 73-189.
RC   STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC   3610 / NRRL NRS-744 / VKM B-501;
RX   PubMed=1901557; DOI=10.1016/0378-1119(91)90110-w;
RA   Sadaie Y., Takamatsu H., Nakamura K., Yamane K.;
RT   "Sequencing reveals similarity of the wild-type div+ gene of Bacillus
RT   subtilis to the Escherichia coli secA gene.";
RL   Gene 98:101-105(1991).
RN   [5]
RP   PROTEIN SEQUENCE OF N-TERMINUS, AND INDUCTION BY SIGB.
RC   STRAIN=168;
RX   PubMed=9296790; DOI=10.1099/00221287-143-3-999;
RA   Bernhardt J., Volker U., Volker A., Antelmann H., Schmid R., Mach H.,
RA   Hecker M.;
RT   "Specific and general stress proteins in Bacillus subtilis--a two-
RT   dimensional protein electrophoresis study.";
RL   Microbiology 143:999-1017(1997).
RN   [6]
RP   FUNCTION, INDUCTION BY SIGB AND SIGH, AND DISRUPTION PHENOTYPE.
RC   STRAIN=168 / IS58;
RX   PubMed=9852014; DOI=10.1128/jb.180.24.6674-6680.1998;
RA   Drzewiecki K., Eymann C., Mittenhuber G., Hecker M.;
RT   "The yvyD gene of Bacillus subtilis is under dual control of sigmaB and
RT   sigmaH.";
RL   J. Bacteriol. 180:6674-6680(1998).
RN   [7]
RP   FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, INDUCTION BY SIGH, AND DISRUPTION
RP   PHENOTYPE.
RC   STRAIN=168;
RX   PubMed=22950019; DOI=10.1002/mbo3.16;
RA   Tagami K., Nanamiya H., Kazo Y., Maehashi M., Suzuki S., Namba E.,
RA   Hoshiya M., Hanai R., Tozawa Y., Morimoto T., Ogasawara N., Kageyama Y.,
RA   Ara K., Ozaki K., Yoshida M., Kuroiwa H., Kuroiwa T., Ohashi Y.,
RA   Kawamura F.;
RT   "Expression of a small (p)ppGpp synthetase, YwaC, in the (p)ppGpp(0) mutant
RT   of Bacillus subtilis triggers YvyD-dependent dimerization of ribosome.";
RL   MicrobiologyOpen 1:115-134(2012).
CC   -!- FUNCTION: Required for dimerization of active 70S ribosomes into 100S
CC       ribosomes in stationary phase; 100S ribosomes are translationally
CC       inactive and sometimes present during exponential growth. May not be
CC       the only factor implicated (PubMed:22950019). Might negatively regulate
CC       the activity of the sigma-54 factor (SigL) (PubMed:9852014).
CC       {ECO:0000255|HAMAP-Rule:MF_00839, ECO:0000269|PubMed:22950019,
CC       ECO:0000269|PubMed:9852014}.
CC   -!- SUBUNIT: Interacts with 100S ribosomes. Not associated with 70S
CC       ribosome monomers, about 1 monomer per ribosome (PubMed:22950019).
CC       {ECO:0000255|HAMAP-Rule:MF_00839, ECO:0000269|PubMed:22950019}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00839,
CC       ECO:0000305|PubMed:22950019}.
CC   -!- INDUCTION: Expressed under the dual control of sigma-B (PubMed:9296790)
CC       and sigma-H factors (PubMed:9296790, PubMed:9852014). The sigma-B-
CC       dependent promoter drives expression of yvyD under stress conditions
CC       and after glucose starvation, whereas a sigma-H-dependent promoter is
CC       responsible for yvyD transcription following amino acid depletion
CC       (PubMed:9852014). Also claimed to be under sole control of sigma-H
CC       (PubMed:22950019). {ECO:0000269|PubMed:22950019,
CC       ECO:0000269|PubMed:9296790, ECO:0000269|PubMed:9852014}.
CC   -!- DISRUPTION PHENOTYPE: The expression of a sigL-dependent gene (levD) is
CC       up-regulated two-fold in cells lacking yvyD, but the relative amount of
CC       the sigL transcript is not increased (PubMed:9852014). In cells
CC       overexpressing ppGpp synthase YwaC, deletion of this gene causes loss
CC       of 100S ribosome formation by dimerizing 70S ribosomes
CC       (PubMed:22950019). {ECO:0000269|PubMed:22950019,
CC       ECO:0000269|PubMed:9852014}.
CC   -!- SIMILARITY: Belongs to the HPF/YfiA ribosome-associated protein family.
CC       Long HPF subfamily. {ECO:0000255|HAMAP-Rule:MF_00839,
CC       ECO:0000305|PubMed:22950019}.
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DR   EMBL; Z31376; CAA83251.1; -; Genomic_DNA.
DR   EMBL; U56901; AAC44956.1; -; Genomic_DNA.
DR   EMBL; AL009126; CAB15548.1; -; Genomic_DNA.
DR   EMBL; D10279; BAA01121.1; -; Genomic_DNA.
DR   PIR; I40400; I40400.
DR   RefSeq; NP_391411.1; NC_000964.3.
DR   RefSeq; WP_003228031.1; NZ_JNCM01000033.1.
DR   PDB; 5NJT; EM; 3.80 A; x=1-104.
DR   PDBsum; 5NJT; -.
DR   AlphaFoldDB; P28368; -.
DR   SMR; P28368; -.
DR   IntAct; P28368; 1.
DR   MINT; P28368; -.
DR   STRING; 224308.BSU35310; -.
DR   jPOST; P28368; -.
DR   PaxDb; P28368; -.
DR   PRIDE; P28368; -.
DR   EnsemblBacteria; CAB15548; CAB15548; BSU_35310.
DR   GeneID; 936715; -.
DR   KEGG; bsu:BSU35310; -.
DR   PATRIC; fig|224308.179.peg.3821; -.
DR   eggNOG; COG1544; Bacteria.
DR   InParanoid; P28368; -.
DR   OMA; HGGYGVI; -.
DR   PhylomeDB; P28368; -.
DR   BioCyc; BSUB:BSU35310-MON; -.
DR   Proteomes; UP000001570; Chromosome.
DR   GO; GO:0022627; C:cytosolic small ribosomal subunit; IBA:GO_Central.
DR   GO; GO:0043024; F:ribosomal small subunit binding; IBA:GO_Central.
DR   GO; GO:0043022; F:ribosome binding; IBA:GO_Central.
DR   GO; GO:0045900; P:negative regulation of translational elongation; IBA:GO_Central.
DR   GO; GO:0044238; P:primary metabolic process; IEA:InterPro.
DR   CDD; cd00552; RaiA; 1.
DR   Gene3D; 3.30.160.100; -; 1.
DR   Gene3D; 3.30.505.50; -; 1.
DR   HAMAP; MF_00839; HPF; 1.
DR   InterPro; IPR034694; HPF_long/plastid.
DR   InterPro; IPR036567; RHF-like.
DR   InterPro; IPR003489; RHF/RaiA.
DR   InterPro; IPR032528; Ribosom_S30AE_C.
DR   InterPro; IPR038416; Ribosom_S30AE_C_sf.
DR   Pfam; PF16321; Ribosom_S30AE_C; 1.
DR   Pfam; PF02482; Ribosomal_S30AE; 1.
DR   SUPFAM; SSF69754; SSF69754; 1.
DR   TIGRFAMs; TIGR00741; yfiA; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; Direct protein sequencing; Reference proteome;
KW   Stress response; Translation regulation.
FT   CHAIN           1..189
FT                   /note="Ribosome hibernation promotion factor"
FT                   /id="PRO_0000208589"
SQ   SEQUENCE   189 AA;  21980 MW;  A015EA9095C9CFA3 CRC64;
     MNYNIRGENI EVTPALKDHV ERKIGKLERY FDHSVDADVN VNLKFYNDKE SKVEVTIPMT
     DLALRSEVHN EDMYNAIDLA TNKLERQIRK HKTKVNRKFR EQGSPKYLLA NGLGSDTDIA
     VQDDIEEEES LDIVRQKRFN LKPMDSEEAI LQMNMLGHNF FVFTNAETNL TNVVYRRNDG
     KYGLIEPTE