Elsevier

Gene

Volume 278, Issues 1–2, 31 October 2001, Pages 253-264
Gene

Prokaryotic structural maintenance of chromosomes (SMC) proteins: distribution, phylogeny, and comparison with MukBs and additional prokaryotic and eukaryotic coiled-coil proteins

https://doi.org/10.1016/S0378-1119(01)00733-8Get rights and content

Abstract

Structural maintenance of chromosomes (SMC) proteins are known to be essential for chromosome segregation in some prokaryotes and in eukaryotes. A systematic search for the distribution of SMC proteins in prokaryotes with fully or partially sequenced genomes showed that they form a larger family than previously anticipated and raised the number of known prokaryotic homologs to 54. Secondary structure predictions revealed that the length of the globular N-terminal and C-terminal domains is extremely well conserved in contrast to the hinge domain and coiled-coil domains which are considerably shorter in several bacterial species. SMC proteins are present in all gram-positive bacteria and in nearly all archaea while they were found in less than half of the gram-negative bacteria. Phylogenetic analyses indicate that the SMC tree roughly resembles the 16S rRNA tree, but that cyanobacteria and Aquifex aeolicus obtained smc genes by lateral transfer from archaea. Fourteen out of 22 smc genes located in fully sequenced genomes seem to be co-transcribed with a second gene out of six different gene families, indicating that the deduced gene products might be involved in similar functions. The SMC proteins were compared with other prokaryotic proteins with long coiled-coil domains. The lengths of different protein domains and signature sequences allowed to differentiate SMCs, MukBs, which were found to be confined to gamma proteobacteria, and two subfamilies of COG 0419 including the SbcC nuclease from E. coli. A phylogenetic analysis was performed including the prokaryotic coiled-coil proteins as well as SMCs and Rad18 proteins from selected eukaryotes.

Introduction

Structural maintenance of chromosomes (SMC) proteins are involved in chromosome segregation in prokaryotes and eukaryotes. They are long proteins of generally more than 1000 amino acids and consist of the following five domains (Fig. 1): (1) an N-terminal globular domain, which contains a Walker A motiv, (2) a first coiled-coil domain of several hundred amino acids, (3) a globular domain thought to act as a hinge, (4) a second coiled-coil domain of several hundred amino acids, and (5) a C-terminal globular domain including a conserved so-called DA box comprised of a Walker B and additional motifs. SMC proteins have been shown to bind DNA; this activity has been localized to the C-terminal globular domain and recently also to the second coiled-coil domain (Graumann et al., 1998, Akhmedow et al., 1999). The Walker A and B boxes indicate that SMC proteins might have an ATPase activity, and for a variety of species this has been verified. It could be shown that the activity is stimulated by the presence of DNA (Hirano and Hirano, 1998). The coiled-coil domains mediate dimerization of SMC proteins, prokaryotic SMCs act as homodimers, while eukaryotes contain several SMCs which form specific heterodimers. Electron micrographs of the Bacillus subtilis SMC showed that it dimerizes in an anti-parallel fashion (Melby et al., 1998), and by generalization this is thought to be true also for eukaryotic SMCs. Anti-parallel dimerization results in totally (prokaryotes) or nearly (eukaryotes) symmetrical molecules, which at both ends have the capacity to bind DNA and to hydrolyze ATP. Recently a complex mimicking one end of an SMC dimer has been generated by covalently fusing an N- and a C-terminal domain by an artificial linker. The structure of the complex has been solved and it was verified that the Walker A and B boxes, which in the native structure are on two different polypeptides, are in close vicinity in the complex (Löwe et al., 2001). The globular ends are separated by the coiled-coil domains which behave as stiff rods, separating the globular domains in a stretched conformation by about 100 nm (Melby et al., 1998). The central hinge domain allows movement of the two ‘arms’ with respect to each other, and the different angles observed in a collection of electron micrographs have led to the model that every position between a fully-stretched conformation and a fully-folded conformation, which brings the DNA-binding domains close together, is possible (Melby et al., 1998). Although the molecular mechanism of energy transduction from ATP hydrolysis to protein movement is totally unclear, this is thought to be essential for one of the functions of SMC proteins, the condensation of DNA.

In eukaryotes, SMC proteins are involved not only in the condensation of DNA, but (1) also in cohesion of the sister chromatides after replication until mitotic segregation into the daughter cells, (2) in recombinational repair, and (3) in chromosome copy number-dependent transcriptional regulation in Caenorhabditis elegans (dosage compensation). Eukaryotes contain four different SMCs, which form specific SMC1+3 and SMC2+4 heterodimers. They build complexes together with non-SMC subunits, which are thought to influence the function. The current knowledge about SMC proteins has been summarized in several recent reviews (Hirano, 1999, Strunnikov and Jessberger, 1999, Cobbe and Heck, 2000, Hirano, 2000, Holmes and Cozzarelli, 2000), which focus mainly on the proteins of eukaryotes. A few bacterial SMC proteins have been detected, and until now biochemical or genetic characterizations are available only for the SMCs of Bacillus subtilis and Caulobacter crescentus, where they were shown to be essential for chromosome partitioning (Britton et al., 1998, Moriya et al., 1998, Jensen and Shapiro, 1999). The B. subtilis SMC has recently been shown to be important for the segregation of the replication termini of the chromosome but was found to be dispensable for the segregation of the replication origins (Graumann, 2000).

In archaea, SMC protein genes were detected in fully sequences genomes, and the possible role of archaeal SMC proteins has been discussed by Bernander (1998). Proteins with similarity to SMC proteins have been characterized from Sulfolobus solfataricus (Elie et al., 1997) and from Halobacterium salinarum (Ruepp et al., 1998). It is known that not all prokaryotes contain SMC genes, e.g. Escherichia coli is devoid of an SMC but contains an analogous protein with the same five-domain structure, called MukB. However, the distribution of SMCs in prokaryotes has not been systematically investigated, and widely differing views about the distribution of these proteins among bacteria are propagated (Cobbe and Heck, 2000, Strunnikov and Jessberger, 1999). Therefore, in the present study a systematic search for smc genes in all available (partially) sequenced prokaryotic genomes was performed to clarify how widespread and typical they are in the domains of archaea and bacteria. Furthermore, the phylogeny of prokaryotic SMCs was analyzed and the SMC proteins were compared to other prokaryotic proteins with long coiled-coil domains.

Until now no complex of prokaryotic SMC proteins with other proteins has been isolated and bacterial SMCs are described to act simply as homodimers. However, it seems to be unlikely that a protein that is involved in chromosome partitioning, which is highly regulated in the bacterial cell cycle, can function without specific interactions with other proteins. Therefore the genomic arrangement of prokaryotic smc genes was also analyzed and several candidate proteins which could possibly interact with SMC proteins were identified.

Section snippets

Sequence retrieval and multiple sequence alignments

Protein sequence databases at the European Bioinformatics Institute were searched using their Sequence Retrieval System (SRS6) and FASTA (Pearson, 1990), and the protein sequence database of the National Center for Biotechnology Information was searched with BLAST (Madden et al., 1996). Sequences were formatted for multiple sequence alignments using the text editor Word’98 on a Macintosh, and multiple sequence alignments were created using ClustalW (Thompson et al., 1994) and analyzed using

Distribution of SMC protein genes in prokaryotic genomes

A first goal of this study was to clarify the distribution of SMC proteins in archaea and bacteria by performing a systematic search for their presence in prokaryotes with fully or partially sequenced genomes. As a preparation, SMC sequences from eight archaeal and bacterial species representing different phylogenetic groups were retrieved from protein sequence databases and a multiple sequence alignment was constructed. The following consensus peptide sequence was derived from a well-conserved

Conclusions

The analysis of the distribution and phylogeny of prokaryotic SMCs revealed that they are widespread and present in nearly all archaea and all gram-positive bacteria, but only in less than half of gram-negative bacteria. The likely co-transcription of prokaryotic SMC genes with other genes identifies six candidate proteins which might be involved in cell-cycle specific functions such as chromosome segregation. Eukaryotic smc genes probably evolved from an archaeal precursor by two consecutive

Acknowledgments

I was supported by the Deutsche Forschungsgemeinschaft (DFG) through a Heisenbergstipendium (grant So 264/4). I am grateful to Dieter Oesterhelt for the possibility to search the genome sequence of Halobacterium salinarum prior to its publication.

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