Nomenclature of the genes encoding IHF

Reciprocally rewiring and repositioning the Integration Host Factor (IHF) subunit genes in Salmonella enterica serovar Typhimurium: impacts on physiology and virulence

The Integration Host Factor (IHF) is a heterodimeric nucleoid-associated protein that plays roles in bacterial nucleoid architecture and genome-wide gene regulation. The ihfA and ihfB genes encode the subunits and are located 350 kbp apart, in the Right replichore of the Salmonella chromosome. IHF is composed of one IhfA and one IhfB subunit. Despite this 1 : 1 stoichiometry, MS revealed that IhfB is produced in 2-fold excess over IhfA. We re-engineered Salmonella to exchange reciprocally the protein-coding regions of ihfA and ihfB, such that each relocated protein-encoding region was driven by the expression signals of the other's gene. MS showed that in this 'rewired' strain, IhfA is produced in excess over IhfB, correlating with enhanced stability of the hybrid ihfB-ihfA mRNA that was expressed from the ihfB promoter. Nevertheless, the rewired strain grew at a similar rate to the wild-type and was similar in competitive fitness. However, compared to the wild-type, it was less motile, had growth-phase-specific reductions in SPI-1 and SPI-2 gene expression, and was engulfed at a higher rate by RAW macrophage. Our data show that while exchanging the physical locations of its ihf genes and the rewiring of their regulatory circuitry are well tolerated in Salmonella, genes involved in the production of type 3 secretion systems exhibit dysregulation accompanied by altered phenotypes.

Specialization of the Reiterated Copies of the Heterodimeric Integration Host Factor Genes in Geobacter sulfurreducens

Integration host factor (IHF) is a widely distributed small heterodimeric protein member of the bacterial Nucleoid-Associated Proteins (NAPs), implicated in multiple DNA regulatory processes. IHF recognizes a specific DNA sequence and induces a large bend of the nucleic acid. IHF function has been mainly linked with the regulation of RpoN-dependent promoters, where IHF commonly recognizes a DNA sequence between the enhancer-binding region and the promoter, facilitating a close contact between the upstream bound activator and the promoter bound, RNA polymerase. In most proteobacteria, the genes encoding IHF subunits (ihfA and ihfB) are found in a single copy. However, in some Deltaproteobacteria, like Geobacter sulfurreducens, those genes are duplicated. To date, the functionality of IHF reiterated encoding genes is unknown. In this work, we achieved the functional characterization of the ihfA-1, ihfA-2, ihfB-1, and ihfB-2 from G. sulfurreducens. Unlike the ΔihfA-2 or ΔihfB-1 strains, single gene deletion in ihfA-1 or ihfB-2, provokes an impairment in fumarate and Fe(III) citrate reduction. Accordingly, sqRT-PCR experiments showed that ihfA-1 and ihfB-2 were expressed at higher levels than ihfA-2 and ihfB-1. In addition, RNA-Seq analysis of the ΔihfA-1 and ΔihfB-2 strains revealed a total of 89 and 122 differentially expressed genes, respectively. Furthermore, transcriptional changes in 25 genes were shared in both mutant strains. Among these genes, we confirmed the upregulation of the pilA-repressor, GSU1771, and downregulation of the triheme-cytochrome (pgcA) and the aconitate hydratase (acnA) genes by RT-qPCR. EMSA experiments also demonstrated the direct binding of IHF to the upstream promoter regions of GSU1771, pgcA and acnA. PilA changes in ΔihfA-1 and ΔihfB-2 strains were also verified by immunoblotting. Additionally, heme-staining of subcellular fractions in ΔihfA-1 and ΔihfB-2 strains revealed a remarkable deficit of c-type cytochromes. Overall, our data indicate that at least during fumarate and Fe(III) citrate reduction, the functional IHF regulator is likely assembled by the products of ihfA-1 and ihfB-2. Also, a role of IHF controlling expression of multiple genes (other than RpoN-dependent) affects G. sulfurreducens physiology and extracellular electron transfer.

oriC-encoded instructions for the initiation of bacterial chromosome replication

Replication of the bacterial chromosome initiates at a single origin of replication that is called oriC. This occurs via the concerted action of numerous proteins, including DnaA, which acts as an initiator. The origin sequences vary across species, but all bacterial oriCs contain the information necessary to guide assembly of the DnaA protein complex at oriC, triggering the unwinding of DNA and the beginning of replication. The requisite information is encoded in the unique arrangement of specific sequences called DnaA boxes, which form a framework for DnaA binding and assembly. Other crucial sequences of bacterial origin include DNA unwinding element (DUE, which designates the site at which oriC melts under the influence of DnaA) and binding sites for additional proteins that positively or negatively regulate the initiation process. In this review, we summarize our current knowledge and understanding of the information encoded in bacterial origins of chromosomal replication, particularly in the context of replication initiation and its regulation. We show that oriC encoded instructions allow not only for initiation but also for precise regulation of replication initiation and coordination of chromosomal replication with the cell cycle (also in response to environmental signals). We focus on Escherichia coli, and then expand our discussion to include several other microorganisms in which additional regulatory proteins have been recently shown to be involved in coordinating replication initiation to other cellular processes (e.g., Bacillus, Caulobacter, Helicobacter, Mycobacterium, and Streptomyces). We discuss diversity of bacterial oriC regions with the main focus on roles of individual DNA recognition sequences at oriC in binding the initiator and regulatory proteins as well as the overall impact of these proteins on the formation of initiation complex.

Integration host factor of Mycobacterium tuberculosis, mIHF, compacts DNA by a bending mechanism

The bacterial chromosomal DNA is folded into a compact structure called as ‘nucleoid’ so that the bacterial genome can be accommodated inside the cell. The shape and size of the nucleoid are determined by several factors including DNA supercoiling, macromolecular crowding and nucleoid associated proteins (NAPs). NAPs bind to different sites of the genome in sequence specific or non-sequence specific manner and play an important role in DNA compaction as well as regulation. Until recently, few NAPs have been discovered in mycobacteria owing to poor sequence similarities with other histone-like proteins of eubacteria. Several putative NAPs have now been identified in Mycobacteria on the basis of enriched basic residues or histone-like “PAKK” motifs. Here, we investigate mycobacterial Integration Host Factor (mIHF) for its architectural roles as a NAP using atomic force microscopy and DNA compaction experiments. We demonstrate that mIHF binds DNA in a non-sequence specific manner and compacts it by a DNA bending mechanism. AFM experiments also indicate a dual architectural role for mIHF in DNA compaction as well as relaxation. These results suggest a convergent evolution in the mechanism of E. coli and mycobacterial IHF in DNA compaction.

Pervasive regulation of nucleoid structure and function by nucleoid-associated proteins

Bacterial DNA is organised in a compact nucleoid body that is tightly associated with the coupled transcription and translation of mRNAs. This structure contains abundant DNA-binding proteins which perform both structural and regulatory roles, and, in Escherichia coli, serve to buffer and organise pervasive DNA superhelicity. We argue that NAPs coordinate regulation of gene expression and superhelicity at the global (or chromosomal) and at local (corresponding to promoter activity and genetic recombination) levels.

The effect of IHF on sigmaS selectivity of the phoA and pst promoters of Escherichia coli

The pst operon, a member of the PHO regulon of Escherichia coli, encodes a high-affinity phosphate transport system whose expression is induced when the cells enter a phase of phosphate starvation. The expression of pst is stimulated by the integration host factor (IHF). Transcription of the PHO regulon genes is initiated by the RNA polymerase complexed with sigma (D) (Esigma (D)). Owing to a cytosine residue at position -13 of the pst promoter its transcription can also be initiated by Esigma (S). Here, we show that inactivation of IHF in vivo abolishes the sigma (S)-dependent transcription initiation of the pst operon, indicating that both -13C residue and IHF are required to confer on pst the ability to be transcribed by Esigma (S). Introduction of a -13C residue in the promoter region of phoA, another PHO regulon gene that is not directly affected by IHF, did not affect its exclusive transcription initiation by Esigma (D).

ihfA gene of the bacterium Myxococcus xanthus and its role in activation of carotenoid genes by blue light

Myxococcus xanthus responds to blue light by producing carotenoids. Several regulatory genes are known that participate in the light action mechanism, which leads to the transcriptional activation of the carotenoid genes. We had already reported the isolation of a carotenoid-less, Tn5-induced strain (MR508), whose mutant site was unlinked to the indicated regulatory genes. Here, we show that OmegaMR508::Tn5 affects all known light-inducible promoters in different ways. It blocks the activation of two of them by light but makes the activity of a third one light independent. The OmegaMR508 locus has been cloned and sequenced. The mutation had occurred at the promoter of a gene we propose is the M. xanthus ortholog of ihfA. This encodes the alpha subunit of the histone-like integration host factor protein. An in-frame deletion within ihfA causes the same effects as the OmegaMR508::Tn5 insertion. Like other IhfA proteins, the deduced amino acid sequence of M. xanthus IhfA shows much similarity to HU, another histone-like protein. Sequence comparison data, however, and the finding that the M. xanthus gene is preceded by gene pheT, as happens in other gram-negative bacteria, strongly argue for the proposed orthology relationship. The M. xanthus ihfA gene shows some unusual features, both from structural and physiological points of view. In particular, the protein is predicted to have a unique, long acidic extension at the carboxyl terminus, and it appears to be necessary for normal cell growth and even vital for a certain wild-type strain of M. xanthus.

A quantitative UV laser footprinting analysis of the interaction of IHF with specific binding sites: re-evaluation of the effective concentration of IHF in the cell

The integration host factor (IHF) of Escherichia coli is a major nucleoid-associated protein that binds to specific sites on DNA. Using gel retardation and competition experiments we have estimated that in vitro IHF binds specific sites 1000-10,000 times more tightly than non-specific, chromosomal DNA. We have analyzed the in vitro and in vivo interaction of IHF with three specific binding sites using UV laser footprinting. Because there is a strict correspondence between the intensity of the footprinting signal and the occupancy of a site, we can correlate in vitro association constants with in vivo site occupancy. From the fractional occupancy of various ihf sites in vivo, we then estimate the amount of free IHF in the cell. Exponentially growing cells contain only about 0.7 nM of free IHF, a value 20-fold smaller than the one previously deduced from DMS footprinting. As a consequence low affinity sites are only partially occupied and strong binding sites reach semi-saturation. In stationary phase the concentration of free IHF in the cell increases about sevenfold. These results show that only a very small fraction of total IHF is free in solution. Given the affinity of IHF for non-specific DNA our data imply that a large part of chromosomal DNA is accessible to IHF, and that IHF is a major contributor to chromosomal DNA condensation. The in vivo UV-laser footprinting method is of general interest, because it allows the measurement and the comparison of DNA-protein interactions in vitro and in vivo.

Selected phenotypes of ihf mutants of Escherichia coli

In attempts to identify subunit-specific phenotypes of ihf mutants we analyzed viability, thermoresistance and protein synthesis patterns in ihfA and ihfB mutants and their respective parental strains. Despite some detected differences in the two-dimensional protein patterns, no significant subunit-specific, physiological effects could be observed. Each mutant was less viable and less thermoresistant than the wild type strain. Moreover, in contrast to the wild type the mutants did not reduce global protein synthesis after prolonged culturing. Examination of expression of transcriptional fusions allowed us to demonstrate autoregulation of both genes by IHF. Additional IHF binding sites in the regulatory region of both ihf genes were footprinted.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

The ihf mRNA levels decline as Neisseria gonorrhoeae enters the stationary growth phase

Integration host factor (IHF) is a small heterodimeric DNA binding protein found in all Gram-negative bacteria and is implicated as a transcription cofactor of pilE in Neisseria gonorrhoeae (Hill, S.A., Samuels, D.S., Carlson, J.H., Wilson, J., Hogan, D., Lubke, L., Belland, R.J., 1997. Integration host factor is a transcriptional cofactor of pilE in Neisseria gonorrhoeae. Mol. Microbiol. 23, 649-656). The ihf genes (ihfA and ihfB) were cloned from N. gonorrhoeae through functional complementation of defined Escherichia coli ihf mutants for plating of phage lambda. The predicted aa sequences of each gonococcal IHF polypeptide showed extensive homology to other reported IHF polypeptide sequences. Northern blotting and primer extension analysis defined the tsp for each gene and indicated a disparity in ihfA and ihfB message levels over time, with ihfB mRNA being more abundant throughout the entire growth cycle. Furthermore, both the ihfA and ihfB message levels declined as cells entered the stationary growth phase. Overall, this study reveals several unique features of ihf transcription in the gonococcus which questions whether certain aspects if ihf transcriptional regulation are universally shared by all Gram-negative bacteria.

Integration host factor is required for 1,2-propanediol-dependent transcription of the cob/pdu regulon in Salmonella typhimurium LT2

We show that integration host factor (IHF) is required for the activation of transcription of the cobalamin biosynthetic (cob) and 1,2-propanediol (1,2-PDL) utilization (pdu) operons in Salmonella typhimurium LT2. A lack of IHF affected transcription of the cob/pdu regulon in at least two ways. First, the level of the regulatory protein PocR was decreased in ihfB (formerly himD) mutants, as judged by Western blot analysis with polyclonal antiserum raised against PocR. Second, even when PocR was available, in the absence of IHF, PocR was unable to activate transcription of cob/pdu in response to 1,2-PDL. This result suggested an additional role for IHF in PocR-dependent transcription activation. Consistent with these findings, ihfB mutants of this bacterium were unable to use 1,2-PDL as a carbon or energy source.

Transcriptional pattern of Escherichia coli ihfB (himD) gene expression

Integration host factor (IHF) is a small heterodimer containing subunits encoded by the unlinked ihfA (himA) and ihfB (himD, hip) genes. The transcriptional pattern of ihfB expression in the logarithmic and stationary growth phases was investigated. The ihfB gene is expressed as both monocistronic and polycistronic (hybridizing also to an internal rpsA probe) transcript. The intensity of the polycistronic transcripts, initiated upstream of rpsA, decreased sharply upon growth cessation. In contrast, expression of the monocistronic ihfB transcript strongly increased when cells entered stationary growth phase. The observed growth rate-dependent regulation of the transcription of these transcripts is in agreement with the previously published data about the regulation of the rpsA and ihfB promoters (Pedersen et al., 1984; Aviv et al., 1994).

Structure and function of the Pseudomonas putida integration host factor

Integration host factor (IHF) is a DNA-binding and -bending protein that has been found in a number of gram-negative bacteria. Here we describe the cloning, sequencing, and functional analysis of the genes coding for the two subunits of IHF from Pseudomonas putida. Both the ihfA and ihfB genes of P. putida code for 100-amino-acid-residue polypeptides that are 1 and 6 residues longer than the Escherichia coli IHF subunits, respectively. The P. putida ihfA and ihfB genes can effectively complement E. coli ihf mutants, suggesting that the P. putida IHF subunits can form functional heterodimers with the IHF subunits of E. coli. Analysis of the amino acid differences between the E. coli and P. putida protein sequences suggests that in the evolution of IHF, amino acid changes were mainly restricted to the N-terminal domains and to the extreme C termini. These changes do not interfere with dimer formation or with DNA recognition. We constructed a P. putida mutant strain carrying an ihfA gene knockout and demonstrated that IHF is essential for the expression of the P(U) promoter of the xyl operon of the upper pathway of toluene degradation. It was further shown that the ihfA P. putida mutant strain carrying the TOL plasmid was defective in the degradation of the aromatic model compound benzyl alcohol, proving the unique role of IHF in xyl operon promoter regulation.