The annotated whole-genome sequence of Mycobacterium tuberculosis indicated that Rv1388 (Mtihf) likely encodes a putative 20 kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or organization of mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF-duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg170, Arg171, and Arg173, which might be involved in DNA binding, and a conserved proline (P150) in the tight turn. The phenotypic sensitivity of Escherichia coli ΔihfA and ΔihfB strains to UV and methylmethanesulfonate could be complemented with the wild-type Mtihf, but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, bind with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHFαβ. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes compaction of DNA into nucleoid-like or higher-order filamentous structures. We hence propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

A number of studies have shown that the structure and composition of bacterial nucleoid influences many a processes related to DNA metabolism. The nucleoid-associated proteins modulate not only the DNA conformation but also regulate the DNA metabolic processes such as replication, recombination, repair and transcription. Understanding of how these processes occur in the context of Mycobacterium tuberculosis nucleoid is of considerable medical importance because the nucleoid structure may be constantly remodeled in response to environmental signals and/or growth conditions. Many studies have concluded that Escherichia coli H-NS binds to DNA in a sequence-independent manner, with a preference for A-/T-rich tracts in curved DNA; however, recent studies have identified the existence of medium- and low-affinity binding sites in the vicinity of the curved DNA. Here, we show that the M. tuberculosis H-NS protein binds in a more structure-specific manner to DNA replication and repair intermediates, but displays lower affinity for double-stranded DNA with relatively higher GC content. Notably, M. tuberculosis H-NS was able to bind Holliday junction (HJ), the central recombination intermediate, with substantially higher affinity and inhibited the three-strand exchange promoted by its cognate RecA. Likewise, E. coli H-NS was able to bind the HJ and suppress DNA strand exchange promoted by E. coli RecA, although much less efficiently compared to M. tuberculosis H-NS. Our results provide new insights into a previously unrecognized function of H-NS protein, with implications for blocking the genome integration of horizontally transferred genes by homologous and/or homeologous recombination.

Chickpea is predominantly an indeterminate (IDT) plant due to which high fertility and irrigation have adverse effect on seed yield. The semi-determinate (SDT) types are relatively early, lodging resistant and found to be similar in their yield potential to that of IDT genotypes. However, the inheritance of SDT stem type is not well understood in chickpea. The present investigation was aimed at studying the genetics of SDT stem type and identifying molecular marker linked to Dt1 locus through Bulked Segregant Analysis (BSA). The genetics of semi-determinacy was studied in BGD 72 (IDT) x BG 3078-1(SDT) cross in which the genetic constitution of BGD 72 was already known as Dt1Dt1Dt2Dt2 based on the previous study. The F1 was IDT indicating the dominance of indeterminacy over semideterminacy. The segregation in F2 and F3 revealed that SDT stem growth in the new-found genotype BG3078-1 was governed by a single dominant gene Dt2 and its genotype designated as dt1dt1Dt2Dt2. The study of polymorphic survey between BGD-72(IDT) and BG 3078- 1(SDT) using 581 SSR markers found 50 markers polymorphic. The BSA using 50 polymorphic markers has identified TA42 and TR29 as polymorphic between IDT and SDT parents as well as IDT and SDT bulks and hence considered putatively linked to Dt1 locus governing IDT stem growth in chickpea. The two linked markers were validated in 15 IDT and 15 SDT F2 plants individually. These two markers were also validated in 3 IDT, 8SDT and 3 DT genotypes. This is the first report on the identification of a molecular marker associated with stem growth habit in chickpea.

Authors are urged to introduce these corrections into any reprints they distribute. Secondary (abstract) services are urged to carry notice of these corrections as prominently as they carried the original abstracts.

Background: mIHF belongs to a subfamily of proteins, distinct from E. coli IHF. Results: Functionally important amino acids of mIHF and the mechanism(s) underlying DNA binding, DNA bending, and site-specific recombination are distinct from that of E. coli IHF␣␤. Conclusion: mIHF functions could contribute beyond nucleoid compaction. Significance: Because mIHF is essential for growth, the molecular mechanisms identified here can be exploited in drug screening efforts.

The integration host factor of Mycobacterium tuberculosis (mIHF) consists of a single polypeptide chain, the product of the ihf gene. We previously revealed that mIHF is a novel member of a new class of nucleoid-associated proteins that have important roles in DNA damage response, nucleoid compaction, and integrative recombination. The mIHF contains a region of 86 amino acids at its N terminus, absent from both ␣-and ␤-subunits of Escherichia coli IHF. However, the functional significance of an extra 86-amino-acid region in the full-length protein remains unknown. Here, we report the structure/function relationship of the DNA-binding and integrative recombinationstimulating activity of mIHF. Deletion mutagenesis showed that an extra 86-amino-acid region at the N terminus is dispensable; the C-terminal region possesses the sequences essential for its known biological functions, including the ability to suppress the sensitivity of E. coli ΔihfA and ΔihfB cells to DNA-damaging agents, DNA binding, DNA multimerization-circularization, and stimulation of phage L5 integrase-catalyzed integrative recombination. Single and double alanine substitutions at positions Arg170 and Arg171, located at the mIHF DNA-binding site, abrogated its capacity to suppress the sensitivity of E. coli ⌬ihfA and ΔihfB cells to DNA-damaging agents. The variants encoded by these mutant alleles failed to bind DNA and stimulate integrative recombination. Interestingly, the DNA-binding activity of the mIHF-R173A variant remained largely unaffected; however, it was unable to stimulate integrative recombination, thus revealing a separationof-function allele of mIHF. The functional and structural characterization of this separationof-function allele of mIHF could reveal previously unknown functions of IHF. IMPORTANCEThe integration host factor of Mycobacterium tuberculosis is a novel nucleoid-associated protein. mIHF plays a vital role in DNA damage response, nucleoid compaction, and integrative recombination. Intriguingly, mIHF contains an extra 86-amino-acid region at its N terminus, absent from both ␣-and ␤-subunits of Escherichia coli IHF, whose functional significance is unknown. Furthermore, a triad of arginine residues located at the mIHF-DNA interface have been implicated in a range of its functions. Here, we reveal the roles of N-and C-terminal regions of mIHF and the individual residues in the Arg triad for their ability to provide protection in vivo against DNA damage, bind DNA, and stimulate integrase-catalyzed site-specific recombination.KEYWORDS nucleoid-associated proteins, integration host factor, DNA damage response, integrase, integrative recombination, separation of function T he nucleoid-associated proteins (NAPs) are a set of small, abundant, and generally basic proteins that not only compact the bacterial chromosome and modulate DNA supercoiling but also regulate its structure and influence various cellular processes,

Page 13, Fig. 8B: Lanes 9 to 12 were nonuniformly enhanced. The corrected figure shown below accurately reflects the results in the original image. The correction of this error does not alter the results or conclusions of this article. The lead author apologizes for the need for this correction and takes full responsibility for this inadvertent error. Citation Sharadamma N, Harshavardhana Y, Muniyappa K. 2018. Correction for Sharadamma et al., "Defining the functionally important domain and amino acid residues in Mycobacterium tuberculosis integration host factor for genome stability, DNA binding, and integrative recombination." J Bacteriol 200:e00122-18.