3452
MicroCorrespondence 45
MSEKPL
50
1
M
1
51
TKTDYLMRLRRCQTIDTLERVIEKNKYELSDNELAVFYSAADHRLAELTM
100
2
TKTDYLMRLRKCTTIDTLERVIEKNKYELSDDELELFYSAADHRLAELTM
51
101
NKLYDKIPSSVWKFIR
116
52
NKLYDKIPPTVWQHVK
67
addition to hlyCABD, also contains the 5' upstream hlyR region. Therefore the hha mutation appears to compensate for the absence of hlyR. An additional characteristic of the hha mutation is its pleiotropic effect, increasing the expression of other heterologous proteins cloned in multicopy plasmids (Blanco et al., 1991, FEMS Microbiol Lett 81: 221-226). In a recent paper we reported the cloning of the hha gene and the identification of the Hha protein, a 8.6kDa protein, which appears to modulate haemolysin transcription: hha mutants showed increased levels of the hlyCA transcript (Nieto efa/., 1991, Mo/M;cro£>/o/5:1285-1293). In parallel, Cornelis and co-workers reported the identification and characterization of the ymoA gene of Yersinia enterocolitica (Cornelis ef al., 1991, Mol Microbiol 5: 1023-1034). A comparison of the amino acid sequences of the Hha and YmoA proteins showed 82% identity (Fig. 1). The YmoA protein of Y. enterocolitica regulates the expression of different Y. enterocolitica virulence genes in response to temperature. The ymoA mutants exhibit a phenotype similar to that of hns mutants (Higgins et al., 1990, Mol Microbiol 4: 2007-2012) and it has been suggested that YmoA is a histone-like protein (Cornelis et a/., 1991, ibid.). Both hha and ymoA mutants share some properties, such as pleiotropy (Nieto etal., 1987, ibid.; Cornelis etal., 1991, ibid.), alterations in the topology of the DNA (M. Carmona et al., unpublished; Cornelis et al., 1991; ibid.) and increase of the expression of either the pANN202-312 encoded hly genes or the yop genes at high osmolarity (Carmona etal., unpublished results; Cornelis etal., 1991, ibid). We suggest that both the Hha protein and the YmoA protein are a new class of proteins which modulate bacterial gene expression influencing DNA topology in response to environmental stimuli. F. de la Cruz,^ M. Carmona^ and A. Juarez''* ^Departamento de Microbiologia, Facultad de Biologia, Universidad de Barcelona, Avenida Diagonal 645, 08071 Barcelona, Spain. Tel. (3) 4021486; Fax (3) 4110592.
Fig. 1. Alignment of the Hha (upper level) and YmoA (lower level) proteins using the GAP program with a gap weight of 3.0 and a iength weight of 0.1.
^Departamento de Biologia Molecular, Facultad de Medicina, Universidad de Cantabria, Cardenal Herrera Oria, s/n. 39011 Santander, Spain.
Proposed nomenclature for the genes involved in moiybdenum metaboiism in Escherichia coii and Saimoneiia typhimurium Sir, Several enzymes contain molybdenum cofactor in the form of Mo complexed with molybdopterin (MPT) or molybdopterin guanine dinucleotide (MGD) (Rajagopalan and Johnson, 1992, J Biol Chem 2B7: 10199-10202). Transport of molybdate into the cell and the biosynthesis of molybdenum cofactor require the products of several genes mapping at the different c/7/loci (Bachmann, 1990, Microbiol Rev 54: 130-197; Sanderson and Roth, 1988, Microbiol Rev 52:485-532). The c/7/designation was used to define mutations leading to chlorate resistance, a property initially associated with the lack of nitrate reduction. Subsequently, it was recognized that only mutations in genes for molybdenum cofactor biosynthesis or for molybdate uptake can yield single-step chlorate-resistant mutants (Stewart, 1988, Microbiol Rev 52: 190-232). Assignment of mutations to different chl loci is based on genetic map location and phenotypic characteristics. Nitrate reductase structural genes at the previously designated chic locus have been renamed as nar genes (Bachmann, 1990, Microbiol Rev 54:130-197). However, the pleiotropic chl mutations leading to defects in molybdenum cofactor biosynthesis still retain the chl designation. As we learn more about the genetic complexity of these different chl loci and the biochemistry of molybdenum cofactor biosynthesis, it has become essential that more appropriate gene designations be assigned to the many newly discovered genes. Each one of the chl loci may have more than one gene and use of the existing chl
MicroCorrespondence name to define these genes violates the established convention (Demerec etal., 1966, Genetics54: 61-76). In order to identify the genes involved in molybdenum cofactor biosynthesis unambiguously, we are proposing to abandon the chl nomenclature and adopt a new nomenclature based on the atomic symbol for molybdenum. Mo. We had considered assigning names to the various genes based on the specific biochemical role of each gene product, but these functions are yet to be identified in several cases. We have therefore elected to adopt a straightforward nomenclature which can be implemented for all genes in molybdenum cofactor biosynthesis. This nomenclature will include all genes whose products are essential for molybdate transport into the cell, sequestration and conversion of molybdate ion to the form found in molybdenum cofactor, biosynthesis of MPT and MGD, and assembly of Mo-MPTand Mo-MGD as they exist in the molybdoenzymes. The nomenclature proposed herein for Escherichia co//and Salmonella typhimurium also may be utilized for other organisms.
3453
moa and other c/7/operons will carry the appropriate modesignation. The old and new symbols are presented in Table 1. Any newly discovered operons will carry the next available letter for the third letter extension in the monomenclature, excluding c, f,j, I, m, n, pand f(see Table 1). Several of these designations have been used previously to designate specific chl genes (C, F, J, M, and A/); the gene symbols mop and mof are already used to describe other functions (Bachmann, 1990, Microbiol Rev 54: 130-197; Sanderson and Roth, 1988, Microbiol Rev 52: 485-532) and the designation mol will be used as a collective symbol for molybdenum metabolism genes (see below).
The base symbol for all genes will be mo- and the third letter will be determined using the existing fourth letter of the current chl nomenclature. This avoids confusion and allows uninterrupted carry-over from the chl to monomenclature. Thus, the chIA operon will be designated as
Appropriate gene names can be assigned as more information becomes available on operon structure. For example, the previously designated chlJ gene is the second gene of the mod operon (K.T. Shanmugam ef al., unpublished; R.P. Gunsalus ef al., unpublished) and is thus assigned the name modB. As the complete DNA sequence and genetic characterization of the mod operon become available, the various genes in this operon will carry the appropriate designations [modA, modB, etc.). Likewise, the previously designated chIN and chIM genes are now assigned the names moeB and moaD, respectively (Table 1). The chIG locus was not listed in the most recent E. co//genetic map (Bachmann, 1990, Microbiol Rev 54:130-197) because of an oversight.
Table 1. Old and new designations for the genes involved in moiybdenum metabolism.
Map° Function
New nomenclature
New Operon
Old
chiA" moa moaABCDE
chiB
mob Unknown
17
87
chiCf nar narGHJi cNDf mod modABCD
27 17
chiP
moe moeAB
18
chiG
mog Unknown
a. b. c. d. e.
0
References
MPT synthesis
D. H. Boxer et al. (unpubiished); Rajagopalan and Johnson, 1992, J Biol Chem 267:10199-10202; Stewart, 1988, Microbiol Ftev 52:190-232. MGD synthesis Rajagopalan and Johnson, 1992, J Biol Chem 267:10199-10202; Stewart, 1988, Microbiol Rev 52:190-232. Nitrate reductase Stewart, 1988, Microbiol Rev 52:190-232. Moiybdate uptake R. P. Gunsalus et al. (unpubiished); Johann and Hinton, 1987, J Bacteriol 169:1911-1916; K. T. Shanmugam et ai. (unpublished); Stewart, 1988, Microbiol Rev 52:190-232. MPT synthesis Nohno et al. 1988, J Bacteriol 170:4097-4102; Rajagopaian and Johnson, 1992, J Biol Chem 267:10199-10202; Stewart, 1988, Microbioi Rev 52:190-232. Unknown Rajagopaian and Johnson, 1992, J Bioi Chem 267:10199-10202; Stewart, 1988, Microbiol Rev 52:190-232.
Genetic map position, in minutes. The chlA1 aliele defines the moaA gene, and the chiM mutation defines the moaD gene. The C/7/F mutation was near chIC, probably in the nar region. The originai mutant was iost. The ChlJ gene con-esponds to modB. The chiE5 ailele defines the moeA gene, and the chIN mutation defines the moeB gene.
3454
MicroCorrespondence
Other recommendations We recommend that a mo- designation be assigned only after a detailed analysis of the gene in question, and in the interim the allele name and number should be used to refer to the mutations. One of us (K.T.S.) will serve as a clearing-house for new gene designations. We recommend that the term Mol" be used to designate a molybdenum-defective phenotype, regardless of the symbol of the altered gene. Likewise, we recommend that the term mol be used as a collective symbol for those genes whose products contribute to molybdenum metabolism in the cell, regardless of the gene symbol. These recommendations were agreed to at a recent meeting in Scotland organized by J.A.C. and D.H.B. This letter was inspired by, and is modelled after. Lino ef al. (1988, Microbiol Rev 52: 533-535). K. T. Shanmugam,^ V. Stewart,^ R.P. Gunsalus,^ D. H. Boxer," J. A. Cole,* M. Chippaux,^ J. A. DeMoss,^ G. Giordano,^ E. C. C. Lin^ and K. V. Rajagopalan^ ^Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, USA.
Tel. (904) 392-2490. ^Sections of Microbiology and Genetics & Development, Cornell University, Ithaca, New York 14853, USA. ^Department of Microbiology & Molecular Genetics and Molecular Biology Institute, University of California, Los Angeles, California 90024, USA. ^Department of Biochemistry, University of Dundee, Dundee DD1 4HN, UK. ^School of Biochemistry, University of Birmingham, Birmingham B15 2TT, UK. ^Laboratorie de Chimie Bacterienne, Centre National de la Recherche Scientifique, 13277 Marseille, France. ^Department of Biochemistry & Molecular Biology, University of Texas Medical Center, Houston, Texas 77030, USA. ^Department of Microbiology & Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. ^ Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.
MicroCorrespondence 45
MSEKPL
50
1
M
1
51
TKTDYLMRLRRCQTIDTLERVIEKNKYELSDNELAVFYSAADHRLAELTM
100
2
TKTDYLMRLRKCTTIDTLERVIEKNKYELSDDELELFYSAADHRLAELTM
51
101
NKLYDKIPSSVWKFIR
116
52
NKLYDKIPPTVWQHVK
67
addition to hlyCABD, also contains the 5' upstream hlyR region. Therefore the hha mutation appears to compensate for the absence of hlyR. An additional characteristic of the hha mutation is its pleiotropic effect, increasing the expression of other heterologous proteins cloned in multicopy plasmids (Blanco et al., 1991, FEMS Microbiol Lett 81: 221-226). In a recent paper we reported the cloning of the hha gene and the identification of the Hha protein, a 8.6kDa protein, which appears to modulate haemolysin transcription: hha mutants showed increased levels of the hlyCA transcript (Nieto efa/., 1991, Mo/M;cro£>/o/5:1285-1293). In parallel, Cornelis and co-workers reported the identification and characterization of the ymoA gene of Yersinia enterocolitica (Cornelis ef al., 1991, Mol Microbiol 5: 1023-1034). A comparison of the amino acid sequences of the Hha and YmoA proteins showed 82% identity (Fig. 1). The YmoA protein of Y. enterocolitica regulates the expression of different Y. enterocolitica virulence genes in response to temperature. The ymoA mutants exhibit a phenotype similar to that of hns mutants (Higgins et al., 1990, Mol Microbiol 4: 2007-2012) and it has been suggested that YmoA is a histone-like protein (Cornelis et a/., 1991, ibid.). Both hha and ymoA mutants share some properties, such as pleiotropy (Nieto etal., 1987, ibid.; Cornelis etal., 1991, ibid.), alterations in the topology of the DNA (M. Carmona et al., unpublished; Cornelis et al., 1991; ibid.) and increase of the expression of either the pANN202-312 encoded hly genes or the yop genes at high osmolarity (Carmona etal., unpublished results; Cornelis etal., 1991, ibid). We suggest that both the Hha protein and the YmoA protein are a new class of proteins which modulate bacterial gene expression influencing DNA topology in response to environmental stimuli. F. de la Cruz,^ M. Carmona^ and A. Juarez''* ^Departamento de Microbiologia, Facultad de Biologia, Universidad de Barcelona, Avenida Diagonal 645, 08071 Barcelona, Spain. Tel. (3) 4021486; Fax (3) 4110592.
Fig. 1. Alignment of the Hha (upper level) and YmoA (lower level) proteins using the GAP program with a gap weight of 3.0 and a iength weight of 0.1.
^Departamento de Biologia Molecular, Facultad de Medicina, Universidad de Cantabria, Cardenal Herrera Oria, s/n. 39011 Santander, Spain.
Proposed nomenclature for the genes involved in moiybdenum metaboiism in Escherichia coii and Saimoneiia typhimurium Sir, Several enzymes contain molybdenum cofactor in the form of Mo complexed with molybdopterin (MPT) or molybdopterin guanine dinucleotide (MGD) (Rajagopalan and Johnson, 1992, J Biol Chem 2B7: 10199-10202). Transport of molybdate into the cell and the biosynthesis of molybdenum cofactor require the products of several genes mapping at the different c/7/loci (Bachmann, 1990, Microbiol Rev 54: 130-197; Sanderson and Roth, 1988, Microbiol Rev 52:485-532). The c/7/designation was used to define mutations leading to chlorate resistance, a property initially associated with the lack of nitrate reduction. Subsequently, it was recognized that only mutations in genes for molybdenum cofactor biosynthesis or for molybdate uptake can yield single-step chlorate-resistant mutants (Stewart, 1988, Microbiol Rev 52: 190-232). Assignment of mutations to different chl loci is based on genetic map location and phenotypic characteristics. Nitrate reductase structural genes at the previously designated chic locus have been renamed as nar genes (Bachmann, 1990, Microbiol Rev 54:130-197). However, the pleiotropic chl mutations leading to defects in molybdenum cofactor biosynthesis still retain the chl designation. As we learn more about the genetic complexity of these different chl loci and the biochemistry of molybdenum cofactor biosynthesis, it has become essential that more appropriate gene designations be assigned to the many newly discovered genes. Each one of the chl loci may have more than one gene and use of the existing chl
MicroCorrespondence name to define these genes violates the established convention (Demerec etal., 1966, Genetics54: 61-76). In order to identify the genes involved in molybdenum cofactor biosynthesis unambiguously, we are proposing to abandon the chl nomenclature and adopt a new nomenclature based on the atomic symbol for molybdenum. Mo. We had considered assigning names to the various genes based on the specific biochemical role of each gene product, but these functions are yet to be identified in several cases. We have therefore elected to adopt a straightforward nomenclature which can be implemented for all genes in molybdenum cofactor biosynthesis. This nomenclature will include all genes whose products are essential for molybdate transport into the cell, sequestration and conversion of molybdate ion to the form found in molybdenum cofactor, biosynthesis of MPT and MGD, and assembly of Mo-MPTand Mo-MGD as they exist in the molybdoenzymes. The nomenclature proposed herein for Escherichia co//and Salmonella typhimurium also may be utilized for other organisms.
3453
moa and other c/7/operons will carry the appropriate modesignation. The old and new symbols are presented in Table 1. Any newly discovered operons will carry the next available letter for the third letter extension in the monomenclature, excluding c, f,j, I, m, n, pand f(see Table 1). Several of these designations have been used previously to designate specific chl genes (C, F, J, M, and A/); the gene symbols mop and mof are already used to describe other functions (Bachmann, 1990, Microbiol Rev 54: 130-197; Sanderson and Roth, 1988, Microbiol Rev 52: 485-532) and the designation mol will be used as a collective symbol for molybdenum metabolism genes (see below).
The base symbol for all genes will be mo- and the third letter will be determined using the existing fourth letter of the current chl nomenclature. This avoids confusion and allows uninterrupted carry-over from the chl to monomenclature. Thus, the chIA operon will be designated as
Appropriate gene names can be assigned as more information becomes available on operon structure. For example, the previously designated chlJ gene is the second gene of the mod operon (K.T. Shanmugam ef al., unpublished; R.P. Gunsalus ef al., unpublished) and is thus assigned the name modB. As the complete DNA sequence and genetic characterization of the mod operon become available, the various genes in this operon will carry the appropriate designations [modA, modB, etc.). Likewise, the previously designated chIN and chIM genes are now assigned the names moeB and moaD, respectively (Table 1). The chIG locus was not listed in the most recent E. co//genetic map (Bachmann, 1990, Microbiol Rev 54:130-197) because of an oversight.
Table 1. Old and new designations for the genes involved in moiybdenum metabolism.
Map° Function
New nomenclature
New Operon
Old
chiA" moa moaABCDE
chiB
mob Unknown
17
87
chiCf nar narGHJi cNDf mod modABCD
27 17
chiP
moe moeAB
18
chiG
mog Unknown
a. b. c. d. e.
0
References
MPT synthesis
D. H. Boxer et al. (unpubiished); Rajagopalan and Johnson, 1992, J Biol Chem 267:10199-10202; Stewart, 1988, Microbiol Ftev 52:190-232. MGD synthesis Rajagopalan and Johnson, 1992, J Biol Chem 267:10199-10202; Stewart, 1988, Microbiol Rev 52:190-232. Nitrate reductase Stewart, 1988, Microbiol Rev 52:190-232. Moiybdate uptake R. P. Gunsalus et al. (unpubiished); Johann and Hinton, 1987, J Bacteriol 169:1911-1916; K. T. Shanmugam et ai. (unpublished); Stewart, 1988, Microbiol Rev 52:190-232. MPT synthesis Nohno et al. 1988, J Bacteriol 170:4097-4102; Rajagopaian and Johnson, 1992, J Biol Chem 267:10199-10202; Stewart, 1988, Microbioi Rev 52:190-232. Unknown Rajagopaian and Johnson, 1992, J Bioi Chem 267:10199-10202; Stewart, 1988, Microbiol Rev 52:190-232.
Genetic map position, in minutes. The chlA1 aliele defines the moaA gene, and the chiM mutation defines the moaD gene. The C/7/F mutation was near chIC, probably in the nar region. The originai mutant was iost. The ChlJ gene con-esponds to modB. The chiE5 ailele defines the moeA gene, and the chIN mutation defines the moeB gene.
3454
MicroCorrespondence
Other recommendations We recommend that a mo- designation be assigned only after a detailed analysis of the gene in question, and in the interim the allele name and number should be used to refer to the mutations. One of us (K.T.S.) will serve as a clearing-house for new gene designations. We recommend that the term Mol" be used to designate a molybdenum-defective phenotype, regardless of the symbol of the altered gene. Likewise, we recommend that the term mol be used as a collective symbol for those genes whose products contribute to molybdenum metabolism in the cell, regardless of the gene symbol. These recommendations were agreed to at a recent meeting in Scotland organized by J.A.C. and D.H.B. This letter was inspired by, and is modelled after. Lino ef al. (1988, Microbiol Rev 52: 533-535). K. T. Shanmugam,^ V. Stewart,^ R.P. Gunsalus,^ D. H. Boxer," J. A. Cole,* M. Chippaux,^ J. A. DeMoss,^ G. Giordano,^ E. C. C. Lin^ and K. V. Rajagopalan^ ^Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, USA.
Tel. (904) 392-2490. ^Sections of Microbiology and Genetics & Development, Cornell University, Ithaca, New York 14853, USA. ^Department of Microbiology & Molecular Genetics and Molecular Biology Institute, University of California, Los Angeles, California 90024, USA. ^Department of Biochemistry, University of Dundee, Dundee DD1 4HN, UK. ^School of Biochemistry, University of Birmingham, Birmingham B15 2TT, UK. ^Laboratorie de Chimie Bacterienne, Centre National de la Recherche Scientifique, 13277 Marseille, France. ^Department of Biochemistry & Molecular Biology, University of Texas Medical Center, Houston, Texas 77030, USA. ^Department of Microbiology & Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. ^ Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.
