RRC ID 33711
Author Tanaka K, Henry CS, Zinner JF, Jolivet E, Cohoon MP, Xia F, Bidnenko V, Ehrlich SD, Stevens RL, Noirot P.
Title Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model.
Journal Nucleic Acids Res.
Abstract The nonessential regions in bacterial chromosomes are ill-defined due to incomplete functional information. Here, we establish a comprehensive repertoire of the genome regions that are dispensable for growth of Bacillus subtilis in a variety of media conditions. In complex medium, we attempted deletion of 157 individual regions ranging in size from 2 to 159 kb. A total of 146 deletions were successful in complex medium, whereas the remaining regions were subdivided to identify new essential genes (4) and coessential gene sets (7). Overall, our repertoire covers ~76% of the genome. We screened for viability of mutant strains in rich defined medium and glucose minimal media. Experimental observations were compared with predictions by the iBsu1103 model, revealing discrepancies that led to numerous model changes, including the large-scale application of model reconciliation techniques. We ultimately produced the iBsu1103V2 model and generated predictions of metabolites that could restore the growth of unviable strains. These predictions were experimentally tested and demonstrated to be correct for 27 strains, validating the refinements made to the model. The iBsu1103V2 model has improved considerably at predicting loss of viability, and many insights gained from the model revisions have been integrated into the Model SEED to improve reconstruction of other microbial models.
Volume 41(1)
Pages 687-99
Published 2013-1-7
DOI 10.1093/nar/gks963
PII gks963
PMID 23109554
PMC PMC3592452
MeSH Bacillus subtilis / genetics* Bacillus subtilis / growth & development Bacillus subtilis / metabolism Chromosome Deletion Chromosome Mapping Chromosomes, Bacterial* Metabolic Networks and Pathways / genetics Models, Biological* Phenotype
IF 11.147
Times Cited 27
WOS Category BIOCHEMISTRY & MOLECULAR BIOLOGY
Resource
Prokaryotes B. subtilis JJS-DIn001 JJS-DIn002 JJS-DIn003 JJS-DIn004 JJS-DIn005 JJS-DIn006 JJS-DIn007 JJS-DIn008 JJS-DIn009 JJS-DIn010 JJS-DIn011 JJS-DIn012 JJS-DIn013 JJS-DIn014 JJS-DIn015 JJS-DIn016 JJS-DIn017 JJS-DIn018 JJS-DIn019 JJS-DIn020 JJS-DIn021 JJS-DIn022 JJS-DIn023 JJS-DIn024 JJS-DIn025 JJS-DIn026 JJS-DIn027 JJS-DIn028 JJS-DIn029 JJS-DIn030 JJS-DIn031 JJS-DIn032 JJS-DIn033 JJS-DIn034 JJS-DIn035 JJS-DIn036 JJS-DIn037 JJS-DIn038 JJS-DIn039 JJS-DIn040 JJS-DIn041 JJS-DIn042 JJS-DIn043 JJS-DIn044 JJS-DIn045 JJS-DIn046 JJS-DIn047 JJS-DIn048 JJS-DIn049 JJS-DIn050 JJS-DIn051 JJS-DIn052 JJS-DIn053 JJS-DIn054 JJS-DIn055 JJS-DIn056 JJS-DIn057 JJS-DIn058 JJS-DIn059 JJS-DIn060 JJS-DIn061 JJS-DIn062 JJS-DIn063 JJS-DIn064 JJS-DIn065 JJS-DIn066 JJS-DIn067 JJS-DIn068 JJS-DIn069 JJS-DIn070 JJS-DIn071 JJS-DIn072 JJS-DIn073 JJS-DIn074 JJS-DIn075 JJS-DIn076 JJS-DIn077 JJS-DIn078 JJS-DIn079 JJS-DIn080 JJS-DIn081 JJS-DIn082 JJS-DIn083 JJS-DIn084 JJS-DIn085 JJS-DIn086 JJS-DIn087 JJS-DIn088 JJS-DIn089 JJS-DIn090 JJS-DIn091 JJS-DIn092 JJS-DIn093 JJS-DIn094 JJS-DIn095 JJS-DIn096 JJS-DIn097 JJS-DIn098 JJS-DIn099 JJS-DIn100 JJS-DIn101 JJS-DIn102 JJS-DIn103 JJS-DIn104 JJS-DIn105 JJS-DIn106 JJS-DIn107 JJS-DIn108 JJS-DIn109 JJS-DIn110 JJS-DIn111 JJS-DIn112 JJS-DIn113 JJS-DIn114 JJS-DIn115 JJS-DIn116 JJS-DIn117 JJS-DIn118 JJS-DIn119 JJS-DIn120 JJS-DIn121 JJS-DIn122 JJS-DIn123 JJS-DIn124 JJS-DIn125 JJS-DIn126 JJS-DIn127 JJS-DIn128 JJS-DIn129 JJS-DIn130 JJS-DIn131 JJS-DIn132 JJS-DIn133 JJS-DIn134 JJS-DIn135 JJS-DIn136 JJS-DIn137 JJS-DIn138 JJS-DIn139 JJS-DIn140 JJS-DIn141 JJS-DIn142 JJS-DIn143 JJS-DIn144 JJS-DIn145 JJS-DIn146 JJS-DIn147 JJS-DIn148 JJS-DIn149 JJS-DIn150 JJS-DIn151 JJS-DIn152 JJS-DIn153 JJS-DIn154 JJS-DIn155 JJS-DIn156 JJS-DIn157 JJS-DIn158 JJS-DIn159 JJS-DIn160 JJS-DIn161 JJS-DIn162 JJS-DIn163 JJS-DIn164 JJS-DIn165 JJS-DIn166 JJS-DIn167 JJS-DIn168 JJS-DIn169 JJS-DIn170 JJS-DIn171 JJS-DIn172 JJS-DIn173 JJS-DIn174 JJS-DIn175 JJS-DIn176 JJS-DIn177 JJS-DIn178 JJS-DIn179 JJS-DIn180 JJS-DIn181 JJS-DIn182 JJS-DIn183 JJS-DIn184 JJS-DIn185 JJS-DIn186 JJS-DIn187 JJS-DIn188 JJS-DIn189 JJS-DIn190 JJS-DIn191 JJS-DIn192 JJS-DIn193 JJS-DIn194 JJS-DIn195 JJS-DIn196 JJS-DIn197 JJS-DIn198 JJS-DIn199 JJS-DIn200 JJS-DIn201 JJS-DIn202 JJS-DIn203 JJS-DIn204 JJS-DIn205 JJS-DIn206 JJS-DIn207 JJS-DIn208 JJS-DIn209 JJS-DIn210 JJS-DIn211 JJS-DIn212 JJS-DIn213 JJS-DIn214 JJS-DIn215 JJS-DIn216 JJS-DIn217 JJS-DIn218 JJS-DIn219 JJS-DIn220 JJS-DIn221 JJS-DIn222 JJS-DIn223 JJS-DIn224 JJS-DIn225 JJS-DIn226 JJS-DIn227 JJS-DIn228 JJS-DIn229 JJS-DIn230 JJS-DIn231 JJS-DIn232 JJS-DIn233 JJS-DIn234 JJS-DIn235 JJS-DIn236 JJS-DIn237 JJS-DIn238 JJS-DIn239 JJS-DIn240 JJS-DIn241 JJS-DIn242 JJS-DIn243 JJS-DIn244 JJS-DIn245 JJS-DIn246 JJS-DIn247 JJS-DIn248 JJS-DIn249 JJS-DIn250 JJS-DIn251 JJS-DIn252 JJS-DIn253 JJS-DIn254 JJS-DIn255 JJS-DIn256 JJS-DIn257 JJS-DIn258 JJS-DIn259 JJS-DIn260 JJS-DIn261 JJS-DIn262 JJS-DIn263 JJS-DIn264 JJS-DIn265 JJS-DIn266 JJS-DIn267 JJS-DIn268 JJS-DIn269 JJS-DIn270 JJS-DIn271 JJS-DIn272 JJS-DIn273 JJS-DIn274 JJS-DIn275 JJS-DIn276 JJS-DIn277 JJS-DIn278 JJS-DIn279 JJS-DIn280 JJS-DIn281 JJS-DIn282 JJS-DIn283 JJS-DIn284 JJS-DIn285 JJS-DIn286 JJS-DIn007 JJS-DIn119 JJS-DIn129 duplicated strains MS