Difference between revisions of "Essential genes"

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* There are currently 251 and 2 essential protein and RNA-coding genes, respectively, known in ''B. subtilis''.
  
 +
== An important resource: A knock-down library to study all essential genes ==
 +
We are excited to announce the availability of a new collection of ''Bacillus subtilis'' 168 mutants designed to explore the functions of 289 [[essential genes]] in this organism. The collection is available at the [http://www.bgsc.org/ BGSC].
 +
For details see at the bottom of the page.
 
== Genes in this functional category ==
 
== Genes in this functional category ==
 
=== Protein synthesis, secretion and quality control ===
 
=== Protein synthesis, secretion and quality control ===
Line 22: Line 26:
 
* ''[[alaS]]''
 
* ''[[alaS]]''
 
* ''[[argS]]''
 
* ''[[argS]]''
−
* ''[[asnS]]''
 
 
* ''[[aspS]]''
 
* ''[[aspS]]''
 
* ''[[cysS]]''
 
* ''[[cysS]]''
Line 60: Line 63:
 
* ''[[rplT]]''
 
* ''[[rplT]]''
 
* ''[[rplU]]''
 
* ''[[rplU]]''
 +
* ''[[rplW]]''
 +
* ''[[rplV]]''
 
* ''[[rplX]]''
 
* ''[[rplX]]''
 
* ''[[rpmA]]''
 
* ''[[rpmA]]''
Line 85: Line 90:
 
* ''[[era]]''
 
* ''[[era]]''
 
* ''[[obg]]''
 
* ''[[obg]]''
 +
* ''[[prp]]''
 
* ''[[rbgA]]''
 
* ''[[rbgA]]''
 
* ''[[ysxC]]''
 
* ''[[ysxC]]''
−
* ''[[yqeH]]''
 
−
 
−
==== rRNA modification/maturation ====
 
−
* ''[[cspR]]''
 
−
* ''[[ysgA]]''
 
  
 
==== tRNA modification/maturation ====
 
==== tRNA modification/maturation ====
Line 99: Line 100:
 
* ''[[rnz]]''
 
* ''[[rnz]]''
 
* ''[[cca]]''
 
* ''[[cca]]''
−
* ''[[fmt]]''
 
−
* ''[[folD]]''
 
 
* ''[[trmD]]''
 
* ''[[trmD]]''
 
* ''[[trmU]]''
 
* ''[[trmU]]''
Line 119: Line 118:
  
 
==== Translation/ other ====
 
==== Translation/ other ====
−
* ''[[map]]''
 
 
* ''[[spoVC]]''
 
* ''[[spoVC]]''
  
Line 141: Line 139:
 
* ''[[dapB]]''
 
* ''[[dapB]]''
 
* ''[[dapF]]''
 
* ''[[dapF]]''
 +
* ''[[dapG]]''
 +
* ''[[dapI]]''
 
* ''[[ddl]]''
 
* ''[[ddl]]''
 
* ''[[gcaD]]''
 
* ''[[gcaD]]''
Line 155: Line 155:
 
* ''[[pbpB]]''
 
* ''[[pbpB]]''
 
* ''[[racE]]''
 
* ''[[racE]]''
 +
* ''[[tagA]]''
 
* ''[[tagB]]''
 
* ''[[tagB]]''
 
* ''[[tagD]]''
 
* ''[[tagD]]''
Line 165: Line 166:
 
* ''[[walR]]''
 
* ''[[walR]]''
 
* ''[[ykuQ]]''
 
* ''[[ykuQ]]''
−
* ''[[ykuR]]''
 
  
 
==== Cell division ====
 
==== Cell division ====
Line 173: Line 173:
 
* ''[[ftsL]]''
 
* ''[[ftsL]]''
 
* ''[[ftsW]]''
 
* ''[[ftsW]]''
 +
* ''[[ftsY]]''
 
* ''[[ftsZ]]''
 
* ''[[ftsZ]]''
 
* ''[[mnaA]]''
 
* ''[[mnaA]]''
Line 178: Line 179:
  
 
==== Cell shape ====
 
==== Cell shape ====
 +
* ''[[mbl]]''
 
* ''[[mreB]]''
 
* ''[[mreB]]''
 
* ''[[mreC]]''
 
* ''[[mreC]]''
 
* ''[[mreD]]''
 
* ''[[mreD]]''
 
* ''[[rodA]]''
 
* ''[[rodA]]''
 +
* ''[[rodZ]]''
  
 
=== Metabolism ===
 
=== Metabolism ===
 
==== Central energy metabolism ====
 
==== Central energy metabolism ====
−
* ''[[odhB]]''
 
−
* ''[[pdhA]]''
 
−
* ''[[resB]]''
 
−
* ''[[resC]]''
 
 
* ''[[yumC]]''
 
* ''[[yumC]]''
  
Line 197: Line 196:
  
 
==== Biosynthesis of amino acids ====
 
==== Biosynthesis of amino acids ====
−
* ''[[glyA]]''
+
* ''[[aroE]]''
 
* ''[[metK]]''
 
* ''[[metK]]''
  
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* ''[[fabF]]''
 
* ''[[fabF]]''
 
* ''[[fabG]]''
 
* ''[[fabG]]''
−
* ''[[gpsA]]''
 
 
* ''[[ispC]]''
 
* ''[[ispC]]''
 
* ''[[ispD]]''
 
* ''[[ispD]]''
Line 228: Line 226:
 
* ''[[cmk]]''
 
* ''[[cmk]]''
 
* ''[[gmk]]''
 
* ''[[gmk]]''
−
* ''[[guaB]]''
 
−
* ''[[hprT]]''
 
 
* ''[[nrdE]]''
 
* ''[[nrdE]]''
 
* ''[[nrdF]]''
 
* ''[[nrdF]]''
Line 235: Line 231:
 
* ''[[prs]]''
 
* ''[[prs]]''
 
* ''[[pyrG]]''
 
* ''[[pyrG]]''
 +
* ''[[pyrH]]''
 
* ''[[tmk]]''
 
* ''[[tmk]]''
  
 
==== Biosynthesis of cofactors ====
 
==== Biosynthesis of cofactors ====
 +
* ''[[aroE]]''
 +
* ''[[aroF]]''
 +
* ''[[aroK]]''
 
* ''[[birA]]''
 
* ''[[birA]]''
 +
* ''[[coaD]]''
 +
* ''[[coaBC]]''
 
* ''[[dfrA]]''
 
* ''[[dfrA]]''
 
* ''[[dxs]]''
 
* ''[[dxs]]''
−
* ''[[hepS]]''
+
* ''[[folB]]''
−
* ''[[hepT]]''
+
* ''[[folC]]''
 +
* ''[[folE]]''
 +
* ''[[folK]]''
 
* ''[[menA]]''
 
* ''[[menA]]''
 
* ''[[menB]]''
 
* ''[[menB]]''
Line 248: Line 252:
 
* ''[[menD]]''
 
* ''[[menD]]''
 
* ''[[menE]]''
 
* ''[[menE]]''
−
* ''[[menH]]''
 
 
* ''[[nadD]]''
 
* ''[[nadD]]''
 
* ''[[nadE]]''
 
* ''[[nadE]]''
 
* ''[[nadF]]''
 
* ''[[nadF]]''
 
* ''[[ribC]]''
 
* ''[[ribC]]''
 +
* ''[[sul]]''
 
* ''[[ytaG]]''
 
* ''[[ytaG]]''
  
 
==== Metal ion transport ====
 
==== Metal ion transport ====
−
* ''[[mntA]]''
+
* ''[[mgtE]]''
 
* ''[[mrpA]]''
 
* ''[[mrpA]]''
 
* ''[[mrpB]]''
 
* ''[[mrpB]]''
 
* ''[[mrpC]]''
 
* ''[[mrpC]]''
 
* ''[[mrpD]]''
 
* ''[[mrpD]]''
 +
* ''[[mrpE]]''
 
* ''[[mrpF]]''
 
* ''[[mrpF]]''
 +
* ''[[mrpG]]''
 +
  
 
==== Biosynthesis of iron-sulphur clusters ====
 
==== Biosynthesis of iron-sulphur clusters ====
Line 272: Line 279:
 
==== Phosphate metabolism ====
 
==== Phosphate metabolism ====
 
* ''[[ppaC]]''
 
* ''[[ppaC]]''
−
* ''[[yfkN]]''
 
−
 
  
 
=== DNA replication and chromosome maintenance ===
 
=== DNA replication and chromosome maintenance ===
Line 302: Line 307:
 
* ''[[scpA]]''
 
* ''[[scpA]]''
 
* ''[[smc]]''
 
* ''[[smc]]''
−
* ''[[ypuF]]''
+
* ''[[topA]]''
  
 
=== RNA synthesis and degradation ===
 
=== RNA synthesis and degradation ===
Line 314: Line 319:
 
==== RNases ====
 
==== RNases ====
 
* ''[[rnjA]]''
 
* ''[[rnjA]]''
−
* ''[[rny]]''
 
  
 
=== Protective functions ===
 
=== Protective functions ===
−
* ''[[dgkB]]''
 
−
* ''[[hlpB]]''
 
 
* ''[[pncB]]''
 
* ''[[pncB]]''
 
* ''[[rnc]]''
 
* ''[[rnc]]''
 
* ''[[sknR]]''
 
* ''[[sknR]]''
−
* ''[[sunI]]''
+
* ''[[yezG]]''
 +
* ''[[xre]]''
 
* ''[[ydiO]]''
 
* ''[[ydiO]]''
 
* ''[[ydiP]]''
 
* ''[[ydiP]]''
 
* ''[[yhdL]]''
 
* ''[[yhdL]]''
−
* ''[[ytbE]]''
+
* ''[[yqcF]]''
 
* ''[[yxlC]]''
 
* ''[[yxlC]]''
 +
* ''[[tuaB]]''
 +
* ''[[wapI]]''
 +
* ''[[yxxD]]''
  
 
=== Unknown ===
 
=== Unknown ===
−
* ''[[ycgG]]''
 
 
* ''[[ylaN]]''
 
* ''[[ylaN]]''
 +
* ''[[yneF]]''
 +
* ''[[yqeG]]''
  
 
== [http://subtiliswiki.net/wiki/index.php/Essential_Genes The list of essential genes] according to [http://www.ncbi.nlm.nih.gov/pubmed/12682299 Kobayashi ''et al''. (2003)] ==
 
== [http://subtiliswiki.net/wiki/index.php/Essential_Genes The list of essential genes] according to [http://www.ncbi.nlm.nih.gov/pubmed/12682299 Kobayashi ''et al''. (2003)] ==
 +
 +
== The essential gene knock-down collection ==
 +
The paper describing the construction of this library and its initial characterization will appear in the June 2 edition of Cell. The paper is a collaboration among labs at the University of California, San Francisco, Stanford University, University of California, Berkeley, and McMaster University, Hamilton, Ontario. The co-first authors are Jason M. Peters of UCSF and Alexandre Colavin and Handuo Shi of Stanford.
 +
 +
The library uses a CRISPR interference (CRISPRi) strategy to all a tunable “knockdown” of individual essential genes. Every strain in the library has a Streptococcus pyogenes dcas9 gene integrated into the B. subtilis lacA locus, where it has been placed under control of the xylose-inducible Pxyl promoter. Each strain also has a single-guide RNA (sgRNA) targeting a specific essential gene. The sgRNA coding sequence is integrated into B. subitlis amyE, where it has been placed under the control of the strongly constitutive Pveg promoter. The dCas9 protein lacks nuclease activity. But when dCas9 is present, the sgRNA enables it to bind to the 5’ end of the target gene, where it effectively blocks transcription via steric hindrance. Basal level expression of dcas9 in the absence of xylose knocks down expression of the essential gene about 3-fold. This reduction creates subtle phenotypes, such as increased sensitivity to specific antibiotics and chemical inhibitors, but allows for essentially normal growth under standard laboratory conditions. Full induction of dcas9 with xylose (1%) reduces expression of the essential gene ~150-fold, with drastic consequences for cell morphology and viability. Varying the concentration of xylose between 0.001% and 0.1% allows tunable expression of the essential gene. Peters et al. have not only reported the construction of the library, but have demonstrated its power for analyzing essential genes. They used chemical genomics, for example, to reveal the essential gene network of B. subtilis, revealing interesting connections between seemingly unrelated processes.
 +
 +
These strains provide an invaluable tool for a systematic study of essential genes in a bacterial model system. We thank Jason Peters, Carol Gross, and the entire consortium for donating the library to the BGSC, and we look forward to supplying strains from it to scientists from the B. subtilis research community and beyond. For a complete list of the genes targeted in the library, please see the Peters et al. publication. Summaries of what has been learned previously about most of these genes can be accessed at [SubtiWiki](http://subtiwiki.uni-goettingen.de/wiki/index.php/Essential_genes). It will take a little while for us to update the BGSC online database to include these strains. But their naming convention is simple. The numeric portion of the gene’s locus tag is appended to the prefix “BEC” to produce the strain name. Hence the knockdown strain for the essential gene ligA, which encodes DNA ligase and carries the locus tag BSU06620, is BCE06620. The full genotype of this strain is lacA::Pxyl-dcas9  amyE::Pveg-sgRNA(ligA)  trpC2, and it carries resistance markers for erythromycin and chloramphenicol. Users may request these strains by giving us the targeted gene name or locus tag. Standard user fees apply.
 +
 +
Peters et al., A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria, Cell (2016) {{PubMed|27238023}}
  
 
==Important original publications==
 
==Important original publications==
−
<pubmed>12682299 17114254 17005971 23420519 24178028 </pubmed>
+
<pubmed>12682299 17114254 17005971 23420519 24178028 25092907 27238023 ,28189581</pubmed>
 +
 
 +
==New concepts in essentiality==
 +
<pubmed>32665440</pubmed>
  
 
=Back to [[categories]]=
 
=Back to [[categories]]=

Latest revision as of 16:58, 20 November 2020

Parent category
Neighbouring categories
Related categories

none

  • There are currently 251 and 2 essential protein and RNA-coding genes, respectively, known in B. subtilis.

An important resource: A knock-down library to study all essential genes

We are excited to announce the availability of a new collection of Bacillus subtilis 168 mutants designed to explore the functions of 289 essential genes in this organism. The collection is available at the BGSC. For details see at the bottom of the page.

Genes in this functional category

Protein synthesis, secretion and quality control

Aminoacyl-tRNA synthetases

Ribosomal proteins

Ribosome assembly

tRNA modification/maturation

Translation factors

Translation/ other

Protein secretion/ chaperones/ protein quality control

Cell envelope and cell division

Cell wall synthesis

Cell division

Cell shape

Metabolism

Central energy metabolism

Glycolysis

Biosynthesis of amino acids

Biosynthesis of lipids

Biosynthesis of nucleotides

Biosynthesis of cofactors

Metal ion transport


Biosynthesis of iron-sulphur clusters

Phosphate metabolism

DNA replication and chromosome maintenance

DNA replication

Chromosome condensation/ segregation

RNA synthesis and degradation

Transcription

RNases

Protective functions

Unknown

The list of essential genes according to Kobayashi et al. (2003)

The essential gene knock-down collection

The paper describing the construction of this library and its initial characterization will appear in the June 2 edition of Cell. The paper is a collaboration among labs at the University of California, San Francisco, Stanford University, University of California, Berkeley, and McMaster University, Hamilton, Ontario. The co-first authors are Jason M. Peters of UCSF and Alexandre Colavin and Handuo Shi of Stanford.

The library uses a CRISPR interference (CRISPRi) strategy to all a tunable “knockdown” of individual essential genes. Every strain in the library has a Streptococcus pyogenes dcas9 gene integrated into the B. subtilis lacA locus, where it has been placed under control of the xylose-inducible Pxyl promoter. Each strain also has a single-guide RNA (sgRNA) targeting a specific essential gene. The sgRNA coding sequence is integrated into B. subitlis amyE, where it has been placed under the control of the strongly constitutive Pveg promoter. The dCas9 protein lacks nuclease activity. But when dCas9 is present, the sgRNA enables it to bind to the 5’ end of the target gene, where it effectively blocks transcription via steric hindrance. Basal level expression of dcas9 in the absence of xylose knocks down expression of the essential gene about 3-fold. This reduction creates subtle phenotypes, such as increased sensitivity to specific antibiotics and chemical inhibitors, but allows for essentially normal growth under standard laboratory conditions. Full induction of dcas9 with xylose (1%) reduces expression of the essential gene ~150-fold, with drastic consequences for cell morphology and viability. Varying the concentration of xylose between 0.001% and 0.1% allows tunable expression of the essential gene. Peters et al. have not only reported the construction of the library, but have demonstrated its power for analyzing essential genes. They used chemical genomics, for example, to reveal the essential gene network of B. subtilis, revealing interesting connections between seemingly unrelated processes.

These strains provide an invaluable tool for a systematic study of essential genes in a bacterial model system. We thank Jason Peters, Carol Gross, and the entire consortium for donating the library to the BGSC, and we look forward to supplying strains from it to scientists from the B. subtilis research community and beyond. For a complete list of the genes targeted in the library, please see the Peters et al. publication. Summaries of what has been learned previously about most of these genes can be accessed at [SubtiWiki](http://subtiwiki.uni-goettingen.de/wiki/index.php/Essential_genes). It will take a little while for us to update the BGSC online database to include these strains. But their naming convention is simple. The numeric portion of the gene’s locus tag is appended to the prefix “BEC” to produce the strain name. Hence the knockdown strain for the essential gene ligA, which encodes DNA ligase and carries the locus tag BSU06620, is BCE06620. The full genotype of this strain is lacA::Pxyl-dcas9 amyE::Pveg-sgRNA(ligA) trpC2, and it carries resistance markers for erythromycin and chloramphenicol. Users may request these strains by giving us the targeted gene name or locus tag. Standard user fees apply.

Peters et al., A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria, Cell (2016) PubMed

Important original publications

Byoung-Mo Koo, George Kritikos, Jeremiah D Farelli, Horia Todor, Kenneth Tong, Harvey Kimsey, Ilan Wapinski, Marco Galardini, Angelo Cabal, Jason M Peters, Anna-Barbara Hachmann, David Z Rudner, Karen N Allen, Athanasios Typas, Carol A Gross
Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.
Cell Syst: 2017, 4(3);291-305.e7
[PubMed:28189581] [WorldCat.org] [DOI] (P p)

Jason M Peters, Alexandre Colavin, Handuo Shi, Tomasz L Czarny, Matthew H Larson, Spencer Wong, John S Hawkins, Candy H S Lu, Byoung-Mo Koo, Elizabeth Marta, Anthony L Shiver, Evan H Whitehead, Jonathan S Weissman, Eric D Brown, Lei S Qi, Kerwyn Casey Huang, Carol A Gross
A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria.
Cell: 2016, 165(6);1493-1506
[PubMed:27238023] [WorldCat.org] [DOI] (I p)

Mario Juhas, Daniel R Reuß, Bingyao Zhu, Fabian M Commichau
Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering.
Microbiology (Reading): 2014, 160(Pt 11);2341-2351
[PubMed:25092907] [WorldCat.org] [DOI] (I p)

Raphael H Michna, Fabian M Commichau, Dominik Tödter, Christopher P Zschiedrich, Jörg Stülke
SubtiWiki-a database for the model organism Bacillus subtilis that links pathway, interaction and expression information.
Nucleic Acids Res: 2014, 42(Database issue);D692-8
[PubMed:24178028] [WorldCat.org] [DOI] (I p)

Fabian M Commichau, Nico Pietack, Jörg Stülke
Essential genes in Bacillus subtilis: a re-evaluation after ten years.
Mol Biosyst: 2013, 9(6);1068-75
[PubMed:23420519] [WorldCat.org] [DOI] (I p)

Helena B Thomaides, Ella J Davison, Lisa Burston, Hazel Johnson, David R Brown, Alison C Hunt, Jeffery Errington, Lloyd Czaplewski
Essential bacterial functions encoded by gene pairs.
J Bacteriol: 2007, 189(2);591-602
[PubMed:17114254] [WorldCat.org] [DOI] (P p)

Alison Hunt, Joy P Rawlins, Helena B Thomaides, Jeff Errington
Functional analysis of 11 putative essential genes in Bacillus subtilis.
Microbiology (Reading): 2006, 152(Pt 10);2895-2907
[PubMed:17005971] [WorldCat.org] [DOI] (P p)

K Kobayashi, S D Ehrlich, A Albertini, G Amati, K K Andersen, M Arnaud, K Asai, S Ashikaga, S Aymerich, P Bessieres, F Boland, S C Brignell, S Bron, K Bunai, J Chapuis, L C Christiansen, A Danchin, M Débarbouille, E Dervyn, E Deuerling, K Devine, S K Devine, O Dreesen, J Errington, S Fillinger, S J Foster, Y Fujita, A Galizzi, R Gardan, C Eschevins, T Fukushima, K Haga, C R Harwood, M Hecker, D Hosoya, M F Hullo, H Kakeshita, D Karamata, Y Kasahara, F Kawamura, K Koga, P Koski, R Kuwana, D Imamura, M Ishimaru, S Ishikawa, I Ishio, D Le Coq, A Masson, C Mauël, R Meima, R P Mellado, A Moir, S Moriya, E Nagakawa, H Nanamiya, S Nakai, P Nygaard, M Ogura, T Ohanan, M O'Reilly, M O'Rourke, Z Pragai, H M Pooley, G Rapoport, J P Rawlins, L A Rivas, C Rivolta, A Sadaie, Y Sadaie, M Sarvas, T Sato, H H Saxild, E Scanlan, W Schumann, J F M L Seegers, J Sekiguchi, A Sekowska, S J Séror, M Simon, P Stragier, R Studer, H Takamatsu, T Tanaka, M Takeuchi, H B Thomaides, V Vagner, J M van Dijl, K Watabe, A Wipat, H Yamamoto, M Yamamoto, Y Yamamoto, K Yamane, K Yata, K Yoshida, H Yoshikawa, U Zuber, N Ogasawara
Essential Bacillus subtilis genes.
Proc Natl Acad Sci U S A: 2003, 100(8);4678-83
[PubMed:12682299] [WorldCat.org] [DOI] (P p)


New concepts in essentiality

Larry A Gallagher, Jeannie Bailey, Colin Manoil
Ranking essential bacterial processes by speed of mutant death.
Proc Natl Acad Sci U S A: 2020, 117(30);18010-18017
[PubMed:32665440] [WorldCat.org] [DOI] (I p)


Back to categories

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